From 998ab4e5c34867f5e71055443ddadbb5562879f6 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Wed, 23 Sep 2026 16:26:47 +0000 Subject: [PATCH] Run global analysis methods on simulations (Automated) --- Ranking/DPPC_ranking.csv | 5 ++ Ranking/FF_ranking.csv | 31 ++++--- Ranking/OP_ranking.csv | 11 ++- .../README.yaml | 7 +- .../README.yaml | 11 ++- .../README.yaml | 9 +- .../README.yaml | 7 +- .../README.yaml | 7 +- .../README.yaml | 11 ++- .../README.yaml | 11 ++- .../README.yaml | 8 +- .../README.yaml | 8 +- .../README.yaml | 8 +- .../README.yaml | 11 ++- .../README.yaml | 10 ++- .../README.yaml | 9 +- .../README.yaml | 8 +- .../README.yaml | 12 ++- .../README.yaml | 10 ++- .../README.yaml | 12 ++- .../README.yaml | 10 ++- .../README.yaml | 12 ++- .../README.yaml | 10 ++- .../README.yaml | 9 +- .../README.yaml | 10 ++- .../README.yaml | 10 ++- .../README.yaml | 9 +- .../README.yaml | 8 +- .../README.yaml | 9 +- .../README.yaml | 7 +- .../README.yaml | 11 ++- .../README.yaml 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| 8 +- .../README.yaml | 8 +- .../README.yaml | 12 ++- .../README.yaml | 11 ++- .../README.yaml | 7 +- .../README.yaml | 13 ++- .../README.yaml | 11 ++- .../README.yaml | 8 +- .../README.yaml | 8 +- .../README.yaml | 8 +- .../README.yaml | 12 ++- .../README.yaml | 10 ++- .../README.yaml | 8 +- .../README.yaml | 8 +- .../README.yaml | 8 +- .../README.yaml | 8 +- .../DPPC_FragmentQuality.json | 1 + .../DPPC_OrderParameters_quality.json | 84 +++++++++++++++++++ .../README.yaml | 5 ++ .../SYSTEM_quality.json | 1 + .../README.yaml | 13 ++- .../README.yaml | 10 ++- .../README.yaml | 7 +- .../README.yaml | 11 ++- .../README.yaml | 8 +- .../README.yaml | 8 +- .../README.yaml | 7 +- .../README.yaml | 10 ++- .../README.yaml | 11 ++- .../README.yaml | 8 +- .../README.yaml | 10 ++- .../README.yaml | 7 +- .../README.yaml | 11 ++- .../README.yaml | 8 +- .../README.yaml | 8 +- .../README.yaml | 8 +- .../README.yaml | 8 +- .../README.yaml | 7 +- .../README.yaml | 14 +++- .../README.yaml | 8 +- 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Simulations/144/922/144922f3b678f74edd34e33d582d8e90079353c6/daa44903d8c7513f82d4be1999a50f1157ae679d/FormFactorQuality.json create mode 100644 Simulations/1af/494/1af49498ed5c1f3f8f38daeb37dcd2243c79391e/bb80b1bf80b95dc4fdf84bc17c78e8f7a0000b81/DPPC_FragmentQuality.json create mode 100644 Simulations/1af/494/1af49498ed5c1f3f8f38daeb37dcd2243c79391e/bb80b1bf80b95dc4fdf84bc17c78e8f7a0000b81/DPPC_OrderParameters_quality.json create mode 100644 Simulations/1af/494/1af49498ed5c1f3f8f38daeb37dcd2243c79391e/bb80b1bf80b95dc4fdf84bc17c78e8f7a0000b81/FormFactorQuality.json create mode 100644 Simulations/1af/494/1af49498ed5c1f3f8f38daeb37dcd2243c79391e/bb80b1bf80b95dc4fdf84bc17c78e8f7a0000b81/SYSTEM_quality.json create mode 100644 Simulations/627/f10/627f109a3f0966dd1ac26074c08e55dbf30dc1c3/90ae66b30e033c08b8f754a4a93053086913586e/DPPC_FragmentQuality.json create mode 100644 Simulations/627/f10/627f109a3f0966dd1ac26074c08e55dbf30dc1c3/90ae66b30e033c08b8f754a4a93053086913586e/DPPC_OrderParameters_quality.json create mode 100644 Simulations/627/f10/627f109a3f0966dd1ac26074c08e55dbf30dc1c3/90ae66b30e033c08b8f754a4a93053086913586e/FormFactorQuality.json create mode 100644 Simulations/627/f10/627f109a3f0966dd1ac26074c08e55dbf30dc1c3/90ae66b30e033c08b8f754a4a93053086913586e/SYSTEM_quality.json create mode 100644 Simulations/670/484/6704849a21596a96b4e490419f3c937d719b2904/718296d4c5b00da31a47037e847ab0d5c5246d2c/DPPC_FragmentQuality.json create mode 100644 Simulations/670/484/6704849a21596a96b4e490419f3c937d719b2904/718296d4c5b00da31a47037e847ab0d5c5246d2c/DPPC_OrderParameters_quality.json create mode 100644 Simulations/670/484/6704849a21596a96b4e490419f3c937d719b2904/718296d4c5b00da31a47037e847ab0d5c5246d2c/SYSTEM_quality.json create mode 100644 Simulations/a95/28e/a9528e5501b2b41af2dd6f8540cb514a3eb186e0/5e86893c5c58e183eca1082084085205569a596b/DPPC_FragmentQuality.json create mode 100644 Simulations/a95/28e/a9528e5501b2b41af2dd6f8540cb514a3eb186e0/5e86893c5c58e183eca1082084085205569a596b/DPPC_OrderParameters_quality.json create mode 100644 Simulations/a95/28e/a9528e5501b2b41af2dd6f8540cb514a3eb186e0/5e86893c5c58e183eca1082084085205569a596b/FormFactorQuality.json create mode 100644 Simulations/a95/28e/a9528e5501b2b41af2dd6f8540cb514a3eb186e0/5e86893c5c58e183eca1082084085205569a596b/SYSTEM_quality.json create mode 100644 Simulations/c54/a7f/c54a7fae3f5d01b83d2bdb3d42700185104e05eb/5a9808f2cedaec641ac9f872e539f852c81aa7fc/DPPC_FragmentQuality.json create mode 100644 Simulations/c54/a7f/c54a7fae3f5d01b83d2bdb3d42700185104e05eb/5a9808f2cedaec641ac9f872e539f852c81aa7fc/DPPC_OrderParameters_quality.json create mode 100644 Simulations/c54/a7f/c54a7fae3f5d01b83d2bdb3d42700185104e05eb/5a9808f2cedaec641ac9f872e539f852c81aa7fc/FormFactorQuality.json create mode 100644 Simulations/c54/a7f/c54a7fae3f5d01b83d2bdb3d42700185104e05eb/5a9808f2cedaec641ac9f872e539f852c81aa7fc/SYSTEM_quality.json diff --git a/Ranking/DPPC_ranking.csv b/Ranking/DPPC_ranking.csv index cd2e0e94d0..e8d41a051d 100644 --- a/Ranking/DPPC_ranking.csv +++ b/Ranking/DPPC_ranking.csv @@ -1,6 +1,11 @@ ID,FF,composition,T,Hydration,Q_FF,Q_OP,Q_OP_tails,Q_OP_heads 728,CHARMM36-LJPME,DPPC (1),323.0,31.0,0.7403,0.7976,,0.7976 +935,prosECCo 75 paper related data,DPPC (1),324.0,45.0,0.4525,0.6585,,0.6585 +934,prosECCo 75 paper related data,DPPC (1),322.0,45.0,0.1789,0.6571,,0.6571 +931,prosECCo 75 paper related data,DPPC (1),323.0,45.0,0.4128,0.6561,,0.6561 463,Slipids,DPPC (1),323.0,30.0,0.5802,0.6369,,0.6369 +936,prosECCo 75 paper related data,DPPC (1),321.0,45.0,0.0262,0.6337,,0.6337 +933,prosECCo 75 paper related data,DPPC (1),320.0,45.0,,0.6118,,0.6118 911,CHARMM36,DPPC (1),322.0,41.1,0.2489,0.5992,,0.5992 319,CHARMM36,DPPC (1),323.0,30.4,0.3746,0.5944,,0.5944 390,GAFFlipid,DPPC (1),323.0,30.5,0.3819,0.5881,,0.5881 diff --git a/Ranking/FF_ranking.csv b/Ranking/FF_ranking.csv index ab21e46b2e..ed2d556c4a 100644 --- a/Ranking/FF_ranking.csv +++ b/Ranking/FF_ranking.csv @@ -91,7 +91,9 @@ ID,FF,composition,T,Hydration,Q_FF,Q_OP,Q_OP_tails,Q_OP_heads 47,CHARMM36,DOPC (1),303.15,50.0,0.4967,0.6186,0.607,0.6416 674,MacRog,POPC (1),298.15,50.0,0.493,0.665,0.6968,0.6013 551,CHARMM36,DOPC (1),303.15,50.0,0.4823,0.5898,0.5656,0.6381 +932,prosECCo 75 paper related data,DPPC (1),325.0,45.0,0.4703,,, 457,MacRog,POPC (1),300.0,40.0,0.4673,0.6676,0.6858,0.6312 +935,prosECCo 75 paper related data,DPPC (1),324.0,45.0,0.4525,0.6585,0.0,0.6585 316,CHARMM36,DOPC (1),303.15,50.0,0.4512,0.5558,0.5112,0.6449 87,CHARMM36,DPPC (1),325.0,40.0,0.4412,,, 63,MacRog,POPC (1),298.0,50.0,0.4335,0.5974,0.5853,0.6216 @@ -99,6 +101,7 @@ ID,FF,composition,T,Hydration,Q_FF,Q_OP,Q_OP_tails,Q_OP_heads 702,MacRog,CHOL:POPC (1:4),298.15,50.0,0.4304,,, 533,CHARMM36,POPC (1),303.0,31.1,0.4256,,, 915,CHARMM36/LJ-PME,DLPC (1),293.0,43.1,0.4148,,, +931,prosECCo 75 paper related data,DPPC (1),323.0,45.0,0.4128,0.6561,0.0,0.6561 390,GAFFlipid,DPPC (1),323.0,30.5,0.3819,0.5881,0.0,0.5881 658,MacRog,POPC (1),298.15,50.0,0.3818,0.6963,0.707,0.6749 319,CHARMM36,DPPC (1),323.0,30.4,0.3746,0.5944,0.0,0.5944 @@ -133,6 +136,7 @@ ID,FF,composition,T,Hydration,Q_FF,Q_OP,Q_OP_tails,Q_OP_heads 790,Charmm36,POPE (1),310.0,40.0,0.2055,0.1891,0.0974,0.3724 687,Slipids,CHOL:POPC (1:4),298.15,50.0,0.2024,,, 914,CHARMM36/LJ-PME,DLPC (1),303.0,43.1,0.1916,,, +934,prosECCo 75 paper related data,DPPC (1),322.0,45.0,0.1789,0.6571,0.0,0.6571 27,CHARMM36,DPPC (1),333.15,50.0,0.1766,0.1136,0.0,0.1136 299,Berger and Modified Höltje model for cholesterol,CHOL:POPC (1:1),298.0,80.6,0.1698,0.1702,0.1953,0.0083 305,Berger and Modified Höltje model for cholesterol,CHOL:POPC (1:15),298.0,57.0,0.1603,0.3775,0.5603,0.0118 @@ -162,6 +166,7 @@ ID,FF,composition,T,Hydration,Q_FF,Q_OP,Q_OP_tails,Q_OP_heads 202,GROMOS-CKP,POPC (1),298.0,50.0,0.0367,0.1282,0.1742,0.0362 109,CHARMM36,CHOL:POPC (1:8),298.15,50.0,0.0337,,, 837,FF-development,POPC (1),300.0,40.0,0.0324,0.5638,0.5676,0.5561 +936,prosECCo 75 paper related data,DPPC (1),321.0,45.0,0.0262,0.6337,0.0,0.6337 673,Lipid17,CHOL:POPC (5:8),298.15,50.0,0.0189,,, 694,Lipid17,CHOL:POPC (5:8),298.15,50.0,0.0179,,, 678,CHARMM36,POPC (1),298.15,50.0,0.016,0.3912,0.2693,0.6351 @@ -179,32 +184,32 @@ ID,FF,composition,T,Hydration,Q_FF,Q_OP,Q_OP_tails,Q_OP_heads 833,FF-development,POPC (1),300.0,40.0,0.0029,0.2948,0.1773,0.5299 761,OpenFF,POPC (1),300.0,39.1,0.0019,0.568,0.5584,0.5872 679,MacRog,CHOL:POPC (5:8),298.15,50.0,0.0015,,, -82,slipids,CHOL:POPC (1:1),298.0,39.7,0.0014,0.4174,0.3907,0.1765 72,CHARMM36,CHOL:POPC (1:4),298.15,50.0,0.0014,,, -832,FF-development,POPC (1),300.0,40.0,0.0007,0.2767,0.1768,0.4766 +82,slipids,CHOL:POPC (1:1),298.0,39.7,0.0014,0.4174,0.3907,0.1765 550,CHARMM36,CHOL:POPC (5:8),298.15,50.0,0.0007,,, 716,MacRog,CHOL:POPC (5:8),298.15,50.0,0.0007,,, +832,FF-development,POPC (1),300.0,40.0,0.0007,0.2767,0.1768,0.4766 525,CHARMM36,CHOL:POPC (1:4),298.15,50.0,0.0006,,, 275,CHARMM36,CHOL:POPC (5:8),298.15,50.0,0.0004,,, -703,Slipids,CHOL:POPC (7:8),298.15,50.0,0.0003,0.3257,0.2892,0.1583 -698,MacRog,CHOL:POPC (5:8),298.15,50.0,0.0003,,, 620,CHARMM36,CHOL:POPC (5:8),298.15,50.0,0.0003,,, -712,Slipids,CHOL:POPC (7:8),298.15,50.0,0.0003,0.36,0.3283,0.1671 682,Slipids,CHOL:POPC (7:8),298.15,50.0,0.0003,0.3653,0.334,0.1681 +698,MacRog,CHOL:POPC (5:8),298.15,50.0,0.0003,,, +712,Slipids,CHOL:POPC (7:8),298.15,50.0,0.0003,0.36,0.3283,0.1671 +703,Slipids,CHOL:POPC (7:8),298.15,50.0,0.0003,0.3257,0.2892,0.1583 792,OpenFF,POPC (1),300.0,39.1,0.0002,0.5635,0.5485,0.5935 836,FF-development,POPC (1),300.0,40.0,0.0001,0.3347,0.4433,0.1176 704,MacRog,CHOL:POPC (7:8),298.15,50.0,0.0001,0.218,0.1541,0.175 -91,CHARMM36,CHOL:POPC (7:8),298.15,50.0,0.0,0.3211,0.2694,0.1776 838,Parsley 1.3.1,POPC (1),300.0,40.0,0.0,0.183,0.0182,0.5127 -166,CHARMM36,CHOL:POPC (7:8),298.15,50.0,0.0,0.3354,0.2842,0.184 834,Sage2.2.0 Espaloma Charges,POPC (1),300.0,40.0,0.0,0.3115,0.1992,0.5361 -717,Lipid17,CHOL:POPC (7:8),298.15,50.0,0.0,0.4908,0.515,0.1699 -707,Lipid17,CHOL:POPC (7:8),298.15,50.0,0.0,0.4431,0.4592,0.1541 -543,CHARMM36,CHOL:POPC (7:8),298.15,50.0,0.0,0.3336,0.2788,0.1866 +765,Charmm36,SM16 (1),328.15,45.0,0.0,0.3412,0.3412,0.0 835,FF-development,POPC (1),300.0,40.0,0.0,0.1023,0.0058,0.2953 +828,Sage 2.2.1,POPC (1),300.0,40.0,0.0,0.3899,0.3101,0.5495 +671,MacRog,CHOL:POPC (7:8),298.15,50.0,0.0,0.3119,0.2321,0.196 +717,Lipid17,CHOL:POPC (7:8),298.15,50.0,0.0,0.4908,0.515,0.1699 714,Lipid17,CHOL:POPC (7:8),298.15,50.0,0.0,0.4714,0.4903,0.1653 -765,Charmm36,SM16 (1),328.15,45.0,0.0,0.3412,0.3412,0.0 +91,CHARMM36,CHOL:POPC (7:8),298.15,50.0,0.0,0.3211,0.2694,0.1776 +166,CHARMM36,CHOL:POPC (7:8),298.15,50.0,0.0,0.3354,0.2842,0.184 +543,CHARMM36,CHOL:POPC (7:8),298.15,50.0,0.0,0.3336,0.2788,0.1866 +707,Lipid17,CHOL:POPC (7:8),298.15,50.0,0.0,0.4431,0.4592,0.1541 699,MacRog,CHOL:POPC (7:8),298.15,50.0,0.0,0.2997,0.2274,0.1863 -671,MacRog,CHOL:POPC (7:8),298.15,50.0,0.0,0.3119,0.2321,0.196 731,Charmm-Drude,POPE (1),310.0,35.0,0.0,0.2249,0.3077,0.0593 -828,Sage 2.2.1,POPC (1),300.0,40.0,0.0,0.3899,0.3101,0.5495 diff --git a/Ranking/OP_ranking.csv b/Ranking/OP_ranking.csv index da12e3ed07..7e0fac6a85 100644 --- a/Ranking/OP_ranking.csv +++ b/Ranking/OP_ranking.csv @@ -22,6 +22,9 @@ ID,FF,composition,T,Hydration,Q_FF,Q_OP,Q_OP_tails,Q_OP_heads 674,MacRog,POPC (1),298.15,50.0,0.493,0.665,0.6968,0.6013 800,CHARMM36,DMPC (1),314.0,5.0,,0.66,0.645,0.6901 675,MacRog,POPC (1),298.15,50.0,0.4311,0.659,0.6605,0.6558 +935,prosECCo 75 paper related data,DPPC (1),324.0,45.0,0.4525,0.6585,0.0,0.6585 +934,prosECCo 75 paper related data,DPPC (1),322.0,45.0,0.1789,0.6571,0.0,0.6571 +931,prosECCo 75 paper related data,DPPC (1),323.0,45.0,0.4128,0.6561,0.0,0.6561 715,Lipid17,POPC (1),298.15,50.0,0.8957,0.6511,0.7313,0.4905 806,CHARMM36,POPC (1),300.0,7.5,,0.6489,0.6295,0.6877 809,CHARMM36,DMPC (1),314.0,10.0,,0.6488,0.6504,0.6456 @@ -29,9 +32,11 @@ ID,FF,composition,T,Hydration,Q_FF,Q_OP,Q_OP_tails,Q_OP_heads 696,Slipids,POPC (1),298.15,50.0,0.7477,0.6426,0.669,0.5897 831,C36_Slipids_Hybrid,POPC (1),298.0,50.0,0.2142,0.6389,0.6286,0.6595 463,Slipids,DPPC (1),323.0,30.0,0.5802,0.6369,0.0,0.6369 +936,prosECCo 75 paper related data,DPPC (1),321.0,45.0,0.0262,0.6337,0.0,0.6337 810,OPLS4,DMPC (1),314.0,10.0,,0.6279,0.5503,0.7831 811,OPLS4,DMPC (1),314.0,5.0,,0.6233,0.589,0.6917 47,CHARMM36,DOPC (1),303.15,50.0,0.4967,0.6186,0.607,0.6416 +933,prosECCo 75 paper related data,DPPC (1),320.0,45.0,,0.6118,0.0,0.6118 708,Slipids,POPC (1),298.15,50.0,0.581,0.5997,0.6177,0.5637 911,CHARMM36,DPPC (1),322.0,41.1,0.2489,0.5992,0.0,0.5992 63,MacRog,POPC (1),298.0,50.0,0.4335,0.5974,0.5853,0.6216 @@ -41,8 +46,8 @@ ID,FF,composition,T,Hydration,Q_FF,Q_OP,Q_OP_tails,Q_OP_heads 390,GAFFlipid,DPPC (1),323.0,30.5,0.3819,0.5881,0.0,0.5881 742,AMOEBA,DOPC (1),303.0,40.0,0.3199,0.5814,0.5726,0.5988 813,OPLS4,DMPC (1),314.0,45.0,,0.5752,0.5337,0.6583 -414,Slipids,POPE (1),310.0,50.0,1.0,0.568,0.8488,0.0063 761,OpenFF,POPC (1),300.0,39.1,0.0019,0.568,0.5584,0.5872 +414,Slipids,POPE (1),310.0,50.0,1.0,0.568,0.8488,0.0063 904,CHARMM36m,SD5PC (1),303.15,48.0,,0.5678,0.2839,0.0 924,CHARMM36_charge075_onP_and_on_N,DPPC (1),320.0,45.0,,0.5646,0.0,0.5646 905,CHARMM36m,SD5PC (1),303.15,48.0,,0.5645,0.2823,0.0 @@ -145,10 +150,10 @@ ID,FF,composition,T,Hydration,Q_FF,Q_OP,Q_OP_tails,Q_OP_heads 15,Berger and Modified Höltje model for cholesterol,CHOL:POPC (39:25),298.0,45.2,,0.0413,0.0541,0.0156 472,OPLSAA-compatible Berger-DPPC-06,DPPC (1),323.0,40.0,0.3529,0.0137,0.0,0.0137 41,Berger-DPPC-98,DPPC (1),323.0,40.0,0.6449,0.0105,0.0,0.0105 +503,Lipid17,POPC:POPG (1:1),298.0,105.2,,0.0002,0.0,0.0002 58,CHARMM36,POPC:POPG (175:44),298.0,60.0,,0.0002,0.0,0.0002 307,Slipids,POPC:POPG (1:1),298.0,50.0,,0.0002,0.0,0.0002 -503,Lipid17,POPC:POPG (1:1),298.0,105.2,,0.0002,0.0,0.0002 -146,lipid17ecc,POPC:POPG (1:1),298.0,99.6,,0.0001,0.0,0.0001 592,CHARMM36,POPC:POPG (1:1),298.0,105.0,,0.0001,0.0,0.0001 +146,lipid17ecc,POPC:POPG (1:1),298.0,99.6,,0.0001,0.0,0.0001 429,lipid17ecc,POPC:POPG (175:44),298.0,60.0,,0.0,0.0,0.0 317,lipid17,POPC:POPG (175:44),298.0,60.0,,0.0,0.0,0.0 diff --git a/Simulations/004/eb6/004eb6c414eca4dd73398e7b7218d8961c950b70/21fe6e771571ea659f629e3d2943006de7ff0dde/README.yaml b/Simulations/004/eb6/004eb6c414eca4dd73398e7b7218d8961c950b70/21fe6e771571ea659f629e3d2943006de7ff0dde/README.yaml index 240633b432..029a9142d0 100644 --- a/Simulations/004/eb6/004eb6c414eca4dd73398e7b7218d8961c950b70/21fe6e771571ea659f629e3d2943006de7ff0dde/README.yaml +++ b/Simulations/004/eb6/004eb6c414eca4dd73398e7b7218d8961c950b70/21fe6e771571ea659f629e3d2943006de7ff0dde/README.yaml @@ -45,9 +45,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 236 bioschema_properties: - name: Molecular dynamics trajectory of a POPE bilayer at 303 K (Berger-POPE-2004, GROMACS 4.0.7, 100 ns) [NMRlipids simulation 236] + name: Molecular dynamics trajectory of a POPE bilayer at 303 K (Berger-POPE-2004, + GROMACS 4.0.7, 100 ns) [NMRlipids simulation 236] alternateName: 128POPE_3552SOL_303K_v1 - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) at 303 K. Simulated with Berger-POPE-2004 in GROMACS 4.0.7 for 100 ns (17312 atoms). Deposited as NMRlipids Databank simulation 236 and available from https://doi.org/10.5281/zenodo.1293889. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) + at 303 K. Simulated with Berger-POPE-2004 in GROMACS 4.0.7 for 100 ns (17312 atoms). + Deposited as NMRlipids Databank simulation 236 and available from https://doi.org/10.5281/zenodo.1293889. sameAs: https://doi.org/10.5281/zenodo.1293889 datePublished: '2018-06-20' license: diff --git a/Simulations/006/559/006559139e730fc43b244726992145c2f37a1461/3c99810c45a83b4ba0e54a69fdea8817498a8930/README.yaml b/Simulations/006/559/006559139e730fc43b244726992145c2f37a1461/3c99810c45a83b4ba0e54a69fdea8817498a8930/README.yaml index 459676845b..5905bbe5da 100644 --- a/Simulations/006/559/006559139e730fc43b244726992145c2f37a1461/3c99810c45a83b4ba0e54a69fdea8817498a8930/README.yaml +++ b/Simulations/006/559/006559139e730fc43b244726992145c2f37a1461/3c99810c45a83b4ba0e54a69fdea8817498a8930/README.yaml @@ -49,9 +49,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 345 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (90:10) bilayer at 310.15 K (CHARMM36, GROMACS 5.0, 500 ns) [NMRlipids simulation 345] + name: Molecular dynamics trajectory of a POPC/CHOL (90:10) bilayer at 310.15 K (CHARMM36, + GROMACS 5.0, 500 ns) [NMRlipids simulation 345] alternateName: 22CHOL_200POPC_9000SOL_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 90 mol%) and 22 CHOL (cholesterol, 10 mol%) at 310.15 K. Simulated with CHARMM36 in GROMACS 5.0 for 500 ns (55428 atoms). Deposited as NMRlipids Databank simulation 345 and available from https://doi.org/10.5281/zenodo.3237420. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 90 mol%) and 22 CHOL (cholesterol, 10 mol%) at 310.15 K. Simulated with CHARMM36 + in GROMACS 5.0 for 500 ns (55428 atoms). Deposited as NMRlipids Databank simulation + 345 and available from https://doi.org/10.5281/zenodo.3237420. sameAs: https://doi.org/10.5281/zenodo.3237420 datePublished: '2016-10-09' license: @@ -140,7 +144,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3237420 identifier: 10.5281/zenodo.3237420 url: https://doi.org/10.5281/zenodo.3237420 - name: POPC with 0, 10, 20, and 30 mol-% of cholesterol at 310 K. Charmm36 force field. + name: POPC with 0, 10, 20, and 30 mol-% of cholesterol at 310 K. Charmm36 force + field. publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/007/494/007494777cfaf4a3bbaf66335df4b9aa48c990e0/542f342c6c9c1b0647bcb98de53be96d5af4b505/README.yaml b/Simulations/007/494/007494777cfaf4a3bbaf66335df4b9aa48c990e0/542f342c6c9c1b0647bcb98de53be96d5af4b505/README.yaml index 04ca0b0203..462561a839 100644 --- a/Simulations/007/494/007494777cfaf4a3bbaf66335df4b9aa48c990e0/542f342c6c9c1b0647bcb98de53be96d5af4b505/README.yaml +++ b/Simulations/007/494/007494777cfaf4a3bbaf66335df4b9aa48c990e0/542f342c6c9c1b0647bcb98de53be96d5af4b505/README.yaml @@ -49,9 +49,14 @@ SOFTWARE: gromacs DIR_WRK: /usr/home/bort/Databank ID: 511 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (55:22:22) bilayer at 310 K (Slipids for lipids, Kohagen for NaCl, GROMACS 4.6, 100 ns) [NMRlipids simulation 511] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (55:22:22) bilayer at 310 + K (Slipids for lipids, Kohagen for NaCl, GROMACS 4.6, 100 ns) [NMRlipids simulation + 511] alternateName: 200POPC_9000SOL_81SOD_81CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 55 mol%), 81 CLA (22 mol%) and 81 SOD (22 mol%) at 310 K. Simulated with Slipids for lipids, Kohagen for NaCl in GROMACS 4.6 for 100 ns (53962 atoms). Deposited as NMRlipids Databank simulation 511 and available from https://doi.org/10.5281/zenodo.35193. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 55 mol%), 81 CLA (22 mol%) and 81 SOD (22 mol%) at 310 K. Simulated with Slipids + for lipids, Kohagen for NaCl in GROMACS 4.6 for 100 ns (53962 atoms). Deposited + as NMRlipids Databank simulation 511 and available from https://doi.org/10.5281/zenodo.35193. sameAs: https://doi.org/10.5281/zenodo.35193 datePublished: '2015-12-11' license: diff --git a/Simulations/007/ed1/007ed172073ee268b07f29ecd413eb9de13a3d47/895cd634e9106b949e0c15cd8873592748b66fed/README.yaml b/Simulations/007/ed1/007ed172073ee268b07f29ecd413eb9de13a3d47/895cd634e9106b949e0c15cd8873592748b66fed/README.yaml index 65ab11ae16..e8cdce34b4 100644 --- a/Simulations/007/ed1/007ed172073ee268b07f29ecd413eb9de13a3d47/895cd634e9106b949e0c15cd8873592748b66fed/README.yaml +++ b/Simulations/007/ed1/007ed172073ee268b07f29ecd413eb9de13a3d47/895cd634e9106b949e0c15cd8873592748b66fed/README.yaml @@ -44,9 +44,12 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 512 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 313 K (CHARMM36, GROMACS 5, 200 ns) [NMRlipids simulation 512] + name: Molecular dynamics trajectory of a POPC bilayer at 313 K (CHARMM36, GROMACS + 5, 200 ns) [NMRlipids simulation 512] alternateName: 200POPC_9000SOL_313K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 313 K. Simulated with CHARMM36 in GROMACS 5 for 200 ns (53800 atoms). Deposited as NMRlipids Databank simulation 512 and available from https://doi.org/10.5281/zenodo.4040423. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 313 K. Simulated with CHARMM36 in GROMACS 5 for 200 ns (53800 atoms). Deposited + as NMRlipids Databank simulation 512 and available from https://doi.org/10.5281/zenodo.4040423. sameAs: https://doi.org/10.5281/zenodo.4040423 datePublished: '2020-09-21' license: diff --git a/Simulations/016/283/0162831e71a4b86478b4c1a302886f094fe156a7/13397d54f5210854bef5a1f1f71677131ba01729/README.yaml b/Simulations/016/283/0162831e71a4b86478b4c1a302886f094fe156a7/13397d54f5210854bef5a1f1f71677131ba01729/README.yaml index 2c103265f1..6b9adc2c16 100644 --- a/Simulations/016/283/0162831e71a4b86478b4c1a302886f094fe156a7/13397d54f5210854bef5a1f1f71677131ba01729/README.yaml +++ b/Simulations/016/283/0162831e71a4b86478b4c1a302886f094fe156a7/13397d54f5210854bef5a1f1f71677131ba01729/README.yaml @@ -45,9 +45,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 809 bioschema_properties: - name: Molecular dynamics trajectory of a DMPC bilayer at 314 K (CHARMM36, GROMACS 2022.2, 450 ns) [NMRlipids simulation 809] + name: Molecular dynamics trajectory of a DMPC bilayer at 314 K (CHARMM36, GROMACS + 2022.2, 450 ns) [NMRlipids simulation 809] alternateName: 200DMPC_2kSOL_300K - description: Molecular dynamics trajectory of a lipid bilayer of 200 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) at 314 K. Simulated with CHARMM36 in GROMACS 2022.2 for 450 ns (29600 atoms). Deposited as NMRlipids Databank simulation 809 and available from https://doi.org/10.5281/zenodo.10952764. + description: Molecular dynamics trajectory of a lipid bilayer of 200 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) + at 314 K. Simulated with CHARMM36 in GROMACS 2022.2 for 450 ns (29600 atoms). + Deposited as NMRlipids Databank simulation 809 and available from https://doi.org/10.5281/zenodo.10952764. sameAs: https://doi.org/10.5281/zenodo.10952764 datePublished: '2024-04-10' license: diff --git a/Simulations/019/eb8/019eb8d7691998587faa1e618272a564ff9e697e/577a6cc9d00effd20baf941d520a23d91701352d/README.yaml b/Simulations/019/eb8/019eb8d7691998587faa1e618272a564ff9e697e/577a6cc9d00effd20baf941d520a23d91701352d/README.yaml index cc557769d8..e1f6758d5c 100644 --- a/Simulations/019/eb8/019eb8d7691998587faa1e618272a564ff9e697e/577a6cc9d00effd20baf941d520a23d91701352d/README.yaml +++ b/Simulations/019/eb8/019eb8d7691998587faa1e618272a564ff9e697e/577a6cc9d00effd20baf941d520a23d91701352d/README.yaml @@ -47,9 +47,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 327 bioschema_properties: - name: Molecular dynamics trajectory of a CHOL/POPC (59:41) bilayer at 310 K (MacRog, GROMACS 4.6, 200 ns) [NMRlipids simulation 327] + name: Molecular dynamics trajectory of a CHOL/POPC (59:41) bilayer at 310 K (MacRog, + GROMACS 4.6, 200 ns) [NMRlipids simulation 327] alternateName: 52POPC_76CHOL_6400SOL_310K - description: Molecular dynamics trajectory of a lipid bilayer of 76 CHOL (cholesterol, 59 mol%) and 52 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 41 mol%) at 310 K. Simulated with MacRog in GROMACS 4.6 for 200 ns (31792 atoms). Deposited as NMRlipids Databank simulation 327 and available from https://doi.org/10.5281/zenodo.3252052. + description: Molecular dynamics trajectory of a lipid bilayer of 76 CHOL (cholesterol, + 59 mol%) and 52 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 41 mol%) + at 310 K. Simulated with MacRog in GROMACS 4.6 for 200 ns (31792 atoms). Deposited + as NMRlipids Databank simulation 327 and available from https://doi.org/10.5281/zenodo.3252052. sameAs: https://doi.org/10.5281/zenodo.3252052 datePublished: '2015-01-11' license: @@ -142,7 +146,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3252052 identifier: 10.5281/zenodo.3252052 url: https://doi.org/10.5281/zenodo.3252052 - name: POPC/Cholesterol @ 310K. 0, 10, 40, 50 and 60 mol-% cholesterol. Model by Maciejewski and Rog + name: POPC/Cholesterol @ 310K. 0, 10, 40, 50 and 60 mol-% cholesterol. Model by + Maciejewski and Rog publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/025/f9e/025f9ed451a069ef493a763eeb04d9d84adacb1c/58c3b33bb9325f8d0c3c60fc399e2ddac451ef24/README.yaml b/Simulations/025/f9e/025f9ed451a069ef493a763eeb04d9d84adacb1c/58c3b33bb9325f8d0c3c60fc399e2ddac451ef24/README.yaml index 033cfa9363..9e2bd96d9d 100644 --- a/Simulations/025/f9e/025f9ed451a069ef493a763eeb04d9d84adacb1c/58c3b33bb9325f8d0c3c60fc399e2ddac451ef24/README.yaml +++ b/Simulations/025/f9e/025f9ed451a069ef493a763eeb04d9d84adacb1c/58c3b33bb9325f8d0c3c60fc399e2ddac451ef24/README.yaml @@ -55,9 +55,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 269 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (43:38:19) bilayer at 310 K (Berger, GROMACS 4.5.5, 100 ns) [NMRlipids simulation 269] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (43:38:19) bilayer at 310 + K (Berger, GROMACS 4.5.5, 100 ns) [NMRlipids simulation 269] alternateName: 128POPC_4308SOL_56CAL_112CLA_310K_Berger - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 43 mol%), 112 CLA (38 mol%) and 56 CAL (19 mol%) at 310 K. Simulated with Berger in GROMACS 4.5.5 for 100 ns (19748 atoms). Deposited as NMRlipids Databank simulation 269 and available from https://doi.org/10.5281/zenodo.887396. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 43 mol%), 112 CLA (38 mol%) and 56 CAL (19 mol%) at 310 K. Simulated with Berger + in GROMACS 4.5.5 for 100 ns (19748 atoms). Deposited as NMRlipids Databank simulation + 269 and available from https://doi.org/10.5281/zenodo.887396. sameAs: https://doi.org/10.5281/zenodo.887396 datePublished: '2017-09-07' license: @@ -148,7 +152,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.887396 identifier: 10.5281/zenodo.887396 url: https://doi.org/10.5281/zenodo.887396 - name: Md Simulation Trajectory Of A Popc Bilayer With 716Mm Cacl2, Berger Force Field For Lipids, Scaled Charges For Ca2+ And Cl- + name: Md Simulation Trajectory Of A Popc Bilayer With 716Mm Cacl2, Berger Force + Field For Lipids, Scaled Charges For Ca2+ And Cl- publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/027/fe6/027fe66035161f978c2289b10ed49a435ad1d0fe/d751c636ef8fde62a312b29dfb5a074ae433534b/README.yaml b/Simulations/027/fe6/027fe66035161f978c2289b10ed49a435ad1d0fe/d751c636ef8fde62a312b29dfb5a074ae433534b/README.yaml index beabce5541..fb539672b9 100644 --- a/Simulations/027/fe6/027fe66035161f978c2289b10ed49a435ad1d0fe/d751c636ef8fde62a312b29dfb5a074ae433534b/README.yaml +++ b/Simulations/027/fe6/027fe66035161f978c2289b10ed49a435ad1d0fe/d751c636ef8fde62a312b29dfb5a074ae433534b/README.yaml @@ -56,9 +56,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 221 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/CLA/SOD/CHOL (74:9:9:9) bilayer at 315 K (Slipids, GROMACS, 500 ns) [NMRlipids simulation 221] + name: Molecular dynamics trajectory of a DPPC/CLA/SOD/CHOL (74:9:9:9) bilayer at + 315 K (Slipids, GROMACS, 500 ns) [NMRlipids simulation 221] alternateName: 1032DPPC_120CHOL_46440SOL_124SOD_124CLA_315K - description: Molecular dynamics trajectory of a lipid bilayer of 1032 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 74 mol%), 124 CLA (9 mol%), 124 SOD (9 mol%) and 120 CHOL (cholesterol, 9 mol%) at 315 K. Simulated with Slipids in GROMACS for 500 ns (282608 atoms). Deposited as NMRlipids Databank simulation 221 and available from https://doi.org/10.5281/zenodo.3539263. + description: Molecular dynamics trajectory of a lipid bilayer of 1032 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 74 mol%), 124 CLA (9 mol%), 124 SOD (9 mol%) and 120 CHOL (cholesterol, 9 mol%) + at 315 K. Simulated with Slipids in GROMACS for 500 ns (282608 atoms). Deposited + as NMRlipids Databank simulation 221 and available from https://doi.org/10.5281/zenodo.3539263. sameAs: https://doi.org/10.5281/zenodo.3539263 datePublished: '2019-11-12' license: diff --git a/Simulations/02b/984/02b98418d9965749ac943ecae9627cfdd1dfbdcd/7339faa76da6c93cfee03e59f399e2eed1628b53/README.yaml b/Simulations/02b/984/02b98418d9965749ac943ecae9627cfdd1dfbdcd/7339faa76da6c93cfee03e59f399e2eed1628b53/README.yaml index fd19d6879a..81754184a2 100644 --- a/Simulations/02b/984/02b98418d9965749ac943ecae9627cfdd1dfbdcd/7339faa76da6c93cfee03e59f399e2eed1628b53/README.yaml +++ b/Simulations/02b/984/02b98418d9965749ac943ecae9627cfdd1dfbdcd/7339faa76da6c93cfee03e59f399e2eed1628b53/README.yaml @@ -49,9 +49,13 @@ SOFTWARE: gromacs DIR_WRK: /usr/home/bort/Databank ID: 338 bioschema_properties: - name: Molecular dynamics trajectory of a POPS/SOD (50:50) bilayer at 298 K (Slipids, GROMACS, 100 ns) [NMRlipids simulation 338] + name: Molecular dynamics trajectory of a POPS/SOD (50:50) bilayer at 298 K (Slipids, + GROMACS, 100 ns) [NMRlipids simulation 338] alternateName: 128POPS_4880SOL_128SOD_298K_v2 - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 50 mol%) and 128 SOD (50 mol%) at 298 K. Simulated with Slipids in GROMACS for 100 ns (29824 atoms). Deposited as NMRlipids Databank simulation 338 and available from https://doi.org/10.5281/zenodo.1129441. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, + 50 mol%) and 128 SOD (50 mol%) at 298 K. Simulated with Slipids in GROMACS for + 100 ns (29824 atoms). Deposited as NMRlipids Databank simulation 338 and available + from https://doi.org/10.5281/zenodo.1129441. sameAs: https://doi.org/10.5281/zenodo.1129441 datePublished: '2017-12-24' license: diff --git a/Simulations/02e/922/02e9220d27c2d6f4aa76992ae66014ac8d5557e0/4237bd2c8e11c1b48325386fd672fd6fd3e75894/README.yaml b/Simulations/02e/922/02e9220d27c2d6f4aa76992ae66014ac8d5557e0/4237bd2c8e11c1b48325386fd672fd6fd3e75894/README.yaml index 5387f85082..1df6ee7fa2 100644 --- a/Simulations/02e/922/02e9220d27c2d6f4aa76992ae66014ac8d5557e0/4237bd2c8e11c1b48325386fd672fd6fd3e75894/README.yaml +++ b/Simulations/02e/922/02e9220d27c2d6f4aa76992ae66014ac8d5557e0/4237bd2c8e11c1b48325386fd672fd6fd3e75894/README.yaml @@ -50,9 +50,13 @@ SOFTWARE: gromacs DIR_WRK: /usr/home/bort/Databank ID: 353 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (48:35:17) bilayer at 310.15 K (CHARMM36 with ECC-scaled ions, GROMACS 5.0, 100 ns) [NMRlipids simulation 353] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (48:35:17) bilayer at 310.15 + K (CHARMM36 with ECC-scaled ions, GROMACS 5.0, 100 ns) [NMRlipids simulation 353] alternateName: 200POPC_9000SOL_73CAL_146CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 48 mol%), 146 CLA (35 mol%) and 73 CAL (17 mol%) at 310.15 K. Simulated with CHARMM36 with ECC-scaled ions in GROMACS 5.0 for 100 ns (54019 atoms). Deposited as NMRlipids Databank simulation 353 and available from https://doi.org/10.5281/zenodo.45008. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 48 mol%), 146 CLA (35 mol%) and 73 CAL (17 mol%) at 310.15 K. Simulated with CHARMM36 + with ECC-scaled ions in GROMACS 5.0 for 100 ns (54019 atoms). Deposited as NMRlipids + Databank simulation 353 and available from https://doi.org/10.5281/zenodo.45008. sameAs: https://doi.org/10.5281/zenodo.45008 datePublished: '2016-01-19' license: diff --git a/Simulations/030/bec/030bec1358db2fe351b5f52ba856394ac2b2c35e/e665ce365a39b6e27354a8274706cf6fc1de4716/README.yaml b/Simulations/030/bec/030bec1358db2fe351b5f52ba856394ac2b2c35e/e665ce365a39b6e27354a8274706cf6fc1de4716/README.yaml index c4375b80ec..fe3a8b11e6 100644 --- a/Simulations/030/bec/030bec1358db2fe351b5f52ba856394ac2b2c35e/e665ce365a39b6e27354a8274706cf6fc1de4716/README.yaml +++ b/Simulations/030/bec/030bec1358db2fe351b5f52ba856394ac2b2c35e/e665ce365a39b6e27354a8274706cf6fc1de4716/README.yaml @@ -50,9 +50,13 @@ SOFTWARE: gromacs DIR_WRK: /usr/home/bort/Databank ID: 303 bioschema_properties: - name: Molecular dynamics trajectory of a DAPC/CHOL (81:19) bilayer at 310 K (CHARMM36, GROMACS, 1000 ns) [NMRlipids simulation 303] + name: Molecular dynamics trajectory of a DAPC/CHOL (81:19) bilayer at 310 K (CHARMM36, + GROMACS, 1000 ns) [NMRlipids simulation 303] alternateName: 232DAPC_56CHOL_11520SOL_310K - description: Molecular dynamics trajectory of a lipid bilayer of 232 DAPC (1,2-diarachidonoyl-sn-glycero-3-phosphocholine, 81 mol%) and 56 CHOL (cholesterol, 19 mol%) at 310 K. Simulated with CHARMM36 in GROMACS for 1000 ns (70720 atoms). Deposited as NMRlipids Databank simulation 303 and available from https://doi.org/10.5281/zenodo.2653721. + description: Molecular dynamics trajectory of a lipid bilayer of 232 DAPC (1,2-diarachidonoyl-sn-glycero-3-phosphocholine, + 81 mol%) and 56 CHOL (cholesterol, 19 mol%) at 310 K. Simulated with CHARMM36 + in GROMACS for 1000 ns (70720 atoms). Deposited as NMRlipids Databank simulation + 303 and available from https://doi.org/10.5281/zenodo.2653721. sameAs: https://doi.org/10.5281/zenodo.2653721 datePublished: '2019-04-29' license: @@ -141,7 +145,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.2653721 identifier: 10.5281/zenodo.2653721 url: https://doi.org/10.5281/zenodo.2653721 - name: Atomistic simulations of cholesterol in symmetric lipid bilayers with varying degrees of lipid chain unsaturation + name: Atomistic simulations of cholesterol in symmetric lipid bilayers with varying + degrees of lipid chain unsaturation publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/037/3f2/0373f2b6b97e44c506cb05df82fba09dae77a87e/0cfa263c8b34c52005693282289110536aaf6ee1/README.yaml b/Simulations/037/3f2/0373f2b6b97e44c506cb05df82fba09dae77a87e/0cfa263c8b34c52005693282289110536aaf6ee1/README.yaml index 3124071a23..c5464513e0 100644 --- a/Simulations/037/3f2/0373f2b6b97e44c506cb05df82fba09dae77a87e/0cfa263c8b34c52005693282289110536aaf6ee1/README.yaml +++ b/Simulations/037/3f2/0373f2b6b97e44c506cb05df82fba09dae77a87e/0cfa263c8b34c52005693282289110536aaf6ee1/README.yaml @@ -38,9 +38,12 @@ EXPERIMENT: FORMFACTOR: - 10.1016/j.bbamem.2011.07.022/6 bioschema_properties: - name: Molecular dynamics trajectory of a DLPC bilayer at 293 K (CHARMM36/LJ-PME, GROMACS Gromacs 2022, 100 ns) [NMRlipids simulation 915] + name: Molecular dynamics trajectory of a DLPC bilayer at 293 K (CHARMM36/LJ-PME, + GROMACS Gromacs 2022, 100 ns) [NMRlipids simulation 915] alternateName: Fully hydrated DLPC bilayer in SPC/E water (LJ_cutoff=1.2 nm) - description: Molecular dynamics trajectory of a lipid bilayer of 100 DLPC (1,2-dilauroyl-sn-glycero-3-phosphocholine) at 293 K. Simulated with CHARMM36/LJ-PME in GROMACS Gromacs 2022 for 100 ns (23542 atoms). Deposited as NMRlipids Databank simulation 915 and available from https://doi.org/10.5281/zenodo.20579050. + description: Molecular dynamics trajectory of a lipid bilayer of 100 DLPC (1,2-dilauroyl-sn-glycero-3-phosphocholine) + at 293 K. Simulated with CHARMM36/LJ-PME in GROMACS Gromacs 2022 for 100 ns (23542 + atoms). Deposited as NMRlipids Databank simulation 915 and available from https://doi.org/10.5281/zenodo.20579050. sameAs: https://doi.org/10.5281/zenodo.20579050 datePublished: '2026-06-07' license: @@ -131,7 +134,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.20579050 identifier: 10.5281/zenodo.20579050 url: https://doi.org/10.5281/zenodo.20579050 - name: Fully hydrated DLPC bilayer at different temperatures simulated using CHARMM36 with LJ-PME and LJ-cutoff + name: Fully hydrated DLPC bilayer at different temperatures simulated using CHARMM36 + with LJ-PME and LJ-cutoff publisher: Zenodo _source: api: datacite diff --git a/Simulations/03a/98a/03a98aeace25f568384fe703e1f0d3b4ac01af25/5004da904d772ea193d59c0a0c6a3b830b713816/README.yaml b/Simulations/03a/98a/03a98aeace25f568384fe703e1f0d3b4ac01af25/5004da904d772ea193d59c0a0c6a3b830b713816/README.yaml index f877b1c81d..5fbdcce58e 100644 --- a/Simulations/03a/98a/03a98aeace25f568384fe703e1f0d3b4ac01af25/5004da904d772ea193d59c0a0c6a3b830b713816/README.yaml +++ b/Simulations/03a/98a/03a98aeace25f568384fe703e1f0d3b4ac01af25/5004da904d772ea193d59c0a0c6a3b830b713816/README.yaml @@ -56,9 +56,14 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 474 bioschema_properties: - name: Molecular dynamics trajectory of a CLA/CAL/POPC/POPG (45:25:24:6) bilayer at 298 K (CHARMM36, GROMACS, 200 ns) [NMRlipids simulation 474] + name: Molecular dynamics trajectory of a CLA/CAL/POPC/POPG (45:25:24:6) bilayer + at 298 K (CHARMM36, GROMACS, 200 ns) [NMRlipids simulation 474] alternateName: 400POPC_100POPG_419CAL_738CLA_298K_123398Atoms - description: Molecular dynamics trajectory of a lipid bilayer of 738 CLA (45 mol%), 419 CAL (25 mol%), 400 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 24 mol%) and 100 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 6 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for 200 ns (123398 atoms). Deposited as NMRlipids Databank simulation 474 and available from https://doi.org/10.5281/zenodo.3483785. + description: Molecular dynamics trajectory of a lipid bilayer of 738 CLA (45 mol%), + 419 CAL (25 mol%), 400 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 24 mol%) and 100 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 6 mol%) + at 298 K. Simulated with CHARMM36 in GROMACS for 200 ns (123398 atoms). Deposited + as NMRlipids Databank simulation 474 and available from https://doi.org/10.5281/zenodo.3483785. sameAs: https://doi.org/10.5281/zenodo.3483785 datePublished: '2019-10-12' license: diff --git a/Simulations/03b/07d/03b07d843213f935159d864019a6f66447c50d00/0b554d7564f52c01d95e2ed28411211e3e5d9061/README.yaml b/Simulations/03b/07d/03b07d843213f935159d864019a6f66447c50d00/0b554d7564f52c01d95e2ed28411211e3e5d9061/README.yaml index a9c3ada20b..4749afa9ff 100644 --- a/Simulations/03b/07d/03b07d843213f935159d864019a6f66447c50d00/0b554d7564f52c01d95e2ed28411211e3e5d9061/README.yaml +++ b/Simulations/03b/07d/03b07d843213f935159d864019a6f66447c50d00/0b554d7564f52c01d95e2ed28411211e3e5d9061/README.yaml @@ -49,9 +49,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 655 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (71:29) bilayer at 298.15 K (MacRog, GROMACS 2021, 1001 ns) [NMRlipids simulation 655] + name: Molecular dynamics trajectory of a POPC/CHOL (71:29) bilayer at 298.15 K (MacRog, + GROMACS 2021, 1001 ns) [NMRlipids simulation 655] alternateName: MacRog_POPC_CHOL29_M - description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 71 mol%) and 104 CHOL (cholesterol, 29 mol%) at 298.15 K. Simulated with MacRog in GROMACS 2021 for 1001 ns (96000 atoms). Deposited as NMRlipids Databank simulation 655 and available from https://doi.org/10.5281/zenodo.7061800. + description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 71 mol%) and 104 CHOL (cholesterol, 29 mol%) at 298.15 K. Simulated with MacRog + in GROMACS 2021 for 1001 ns (96000 atoms). Deposited as NMRlipids Databank simulation + 655 and available from https://doi.org/10.5281/zenodo.7061800. sameAs: https://doi.org/10.5281/zenodo.7061800 datePublished: '2022-09-08' license: diff --git a/Simulations/046/3dd/0463dd63f8e46dc2d72690c030c3278e06899b7f/7e4185d7f1994a96d90c25772b0179b27801ea6e/README.yaml b/Simulations/046/3dd/0463dd63f8e46dc2d72690c030c3278e06899b7f/7e4185d7f1994a96d90c25772b0179b27801ea6e/README.yaml index 1554b6e161..5d40af491a 100644 --- a/Simulations/046/3dd/0463dd63f8e46dc2d72690c030c3278e06899b7f/7e4185d7f1994a96d90c25772b0179b27801ea6e/README.yaml +++ b/Simulations/046/3dd/0463dd63f8e46dc2d72690c030c3278e06899b7f/7e4185d7f1994a96d90c25772b0179b27801ea6e/README.yaml @@ -50,9 +50,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 271 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (83:9:9) bilayer at 310 K (Slipids for lipids and Smith & Dang for ions, GROMACS 4.6, 200 ns) [NMRlipids simulation 271] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (83:9:9) bilayer at 310 K + (Slipids for lipids and Smith & Dang for ions, GROMACS 4.6, 200 ns) [NMRlipids + simulation 271] alternateName: 200POPC_9000SOL_21SOD_21CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 83 mol%), 21 CLA (9 mol%) and 21 SOD (9 mol%) at 310 K. Simulated with Slipids for lipids and Smith & Dang for ions in GROMACS 4.6 for 200 ns (53842 atoms). Deposited as NMRlipids Databank simulation 271 and available from https://doi.org/10.5281/zenodo.259335. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 83 mol%), 21 CLA (9 mol%) and 21 SOD (9 mol%) at 310 K. Simulated with Slipids + for lipids and Smith & Dang for ions in GROMACS 4.6 for 200 ns (53842 atoms). + Deposited as NMRlipids Databank simulation 271 and available from https://doi.org/10.5281/zenodo.259335. sameAs: https://doi.org/10.5281/zenodo.259335 datePublished: '2017-01-24' license: @@ -140,7 +145,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.259335 identifier: 10.5281/zenodo.259335 url: https://doi.org/10.5281/zenodo.259335 - name: Popc With Varying Amounts Of Cholesterol, 130 Mm Of Nacl. Slipids With Ions By Smith & Dang + name: Popc With Varying Amounts Of Cholesterol, 130 Mm Of Nacl. Slipids With Ions + By Smith & Dang publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/04a/df9/04adf97610d2ec15af6ea50dcaec6b1bd53e8104/3b2e5a10eb568ea41977bcd1602ae5fb6f2b982a/README.yaml b/Simulations/04a/df9/04adf97610d2ec15af6ea50dcaec6b1bd53e8104/3b2e5a10eb568ea41977bcd1602ae5fb6f2b982a/README.yaml index ed700c931b..3d03f56388 100644 --- a/Simulations/04a/df9/04adf97610d2ec15af6ea50dcaec6b1bd53e8104/3b2e5a10eb568ea41977bcd1602ae5fb6f2b982a/README.yaml +++ b/Simulations/04a/df9/04adf97610d2ec15af6ea50dcaec6b1bd53e8104/3b2e5a10eb568ea41977bcd1602ae5fb6f2b982a/README.yaml @@ -44,9 +44,12 @@ EXPERIMENT: PYPC: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a PYPC bilayer at 333.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 624] + name: Molecular dynamics trajectory of a PYPC bilayer at 333.15 K (CHARMM36, GROMACS, + 1001 ns) [NMRlipids simulation 624] alternateName: 1024PYPC_51200SOL_333K - description: Molecular dynamics trajectory of a lipid bilayer of 1024 PYPC (1-(16:0)-2-(16:1$^\Delta9$)-sn-glycero-3-phosphocholine) at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (284672 atoms). Deposited as NMRlipids Databank simulation 624 and available from https://doi.org/10.5281/zenodo.6943413. + description: Molecular dynamics trajectory of a lipid bilayer of 1024 PYPC (1-(16:0)-2-(16:1$^\Delta9$)-sn-glycero-3-phosphocholine) + at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (284672 atoms). Deposited + as NMRlipids Databank simulation 624 and available from https://doi.org/10.5281/zenodo.6943413. sameAs: https://doi.org/10.5281/zenodo.6943413 datePublished: '2022-07-30' license: @@ -134,7 +137,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.6943413 identifier: 10.5281/zenodo.6943413 url: https://doi.org/10.5281/zenodo.6943413 - name: Simulations of different single-component bilayers, three different system sizes + name: Simulations of different single-component bilayers, three different system + sizes publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/051/412/051412bed812cc77b3a749ee330cd740ab78eeef/051412bed812cc77b3a749ee330cd740ab78eeef/README.yaml b/Simulations/051/412/051412bed812cc77b3a749ee330cd740ab78eeef/051412bed812cc77b3a749ee330cd740ab78eeef/README.yaml index f24b50a3e8..4f7a0b3dcc 100644 --- a/Simulations/051/412/051412bed812cc77b3a749ee330cd740ab78eeef/051412bed812cc77b3a749ee330cd740ab78eeef/README.yaml +++ b/Simulations/051/412/051412bed812cc77b3a749ee330cd740ab78eeef/051412bed812cc77b3a749ee330cd740ab78eeef/README.yaml @@ -49,9 +49,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 451 bioschema_properties: - name: Molecular dynamics trajectory of a CHOL/POPC (50:50) bilayer at 303 K (CHARMM36, OPENMM v7, 100 ns) [NMRlipids simulation 451] + name: Molecular dynamics trajectory of a CHOL/POPC (50:50) bilayer at 303 K (CHARMM36, + OPENMM v7, 100 ns) [NMRlipids simulation 451] alternateName: 80POPC_80CHOL_7200SOL_303K - description: Molecular dynamics trajectory of a lipid bilayer of 80 CHOL (cholesterol, 50 mol%) and 80 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 50 mol%) at 303 K. Simulated with CHARMM36 in OPENMM v7 for 100 ns (38240 atoms). Deposited as NMRlipids Databank simulation 451 and available from https://doi.org/10.5281/zenodo.163345. + description: Molecular dynamics trajectory of a lipid bilayer of 80 CHOL (cholesterol, + 50 mol%) and 80 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 50 mol%) + at 303 K. Simulated with CHARMM36 in OPENMM v7 for 100 ns (38240 atoms). Deposited + as NMRlipids Databank simulation 451 and available from https://doi.org/10.5281/zenodo.163345. sameAs: https://doi.org/10.5281/zenodo.163345 datePublished: '2016-10-26' license: @@ -139,7 +143,9 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.163345 identifier: 10.5281/zenodo.163345 url: https://doi.org/10.5281/zenodo.163345 - name: Popc/Cholesterol (50:50) Lipid Membrane, 303K, Charmm36 Force Field From Charmm-Gui, Simulation Files And 100 Ns Trajectory For Openmm Simulation Engine V7 + name: Popc/Cholesterol (50:50) Lipid Membrane, 303K, Charmm36 Force Field From + Charmm-Gui, Simulation Files And 100 Ns Trajectory For Openmm Simulation Engine + V7 publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/055/759/055759f24d1666a2712316e6a4373ff2737fc73f/a6a93dccf59556c46f05e452a63dc7d30b7653f6/README.yaml b/Simulations/055/759/055759f24d1666a2712316e6a4373ff2737fc73f/a6a93dccf59556c46f05e452a63dc7d30b7653f6/README.yaml index 0ffeb13460..391c6c7692 100644 --- a/Simulations/055/759/055759f24d1666a2712316e6a4373ff2737fc73f/a6a93dccf59556c46f05e452a63dc7d30b7653f6/README.yaml +++ b/Simulations/055/759/055759f24d1666a2712316e6a4373ff2737fc73f/a6a93dccf59556c46f05e452a63dc7d30b7653f6/README.yaml @@ -44,9 +44,12 @@ EXPERIMENT: SOPC: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a SOPC bilayer at 333.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 625] + name: Molecular dynamics trajectory of a SOPC bilayer at 333.15 K (CHARMM36, GROMACS, + 1001 ns) [NMRlipids simulation 625] alternateName: 256SOPC_12800SOL_333K - description: Molecular dynamics trajectory of a lipid bilayer of 256 SOPC (1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (74240 atoms). Deposited as NMRlipids Databank simulation 625 and available from https://doi.org/10.5281/zenodo.6943413. + description: Molecular dynamics trajectory of a lipid bilayer of 256 SOPC (1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (74240 atoms). Deposited + as NMRlipids Databank simulation 625 and available from https://doi.org/10.5281/zenodo.6943413. sameAs: https://doi.org/10.5281/zenodo.6943413 datePublished: '2022-07-30' license: @@ -134,7 +137,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.6943413 identifier: 10.5281/zenodo.6943413 url: https://doi.org/10.5281/zenodo.6943413 - name: Simulations of different single-component bilayers, three different system sizes + name: Simulations of different single-component bilayers, three different system + sizes publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/057/b0e/057b0e7f9930a7ccacd6579adc12edbeb5f6eb2f/2835104546d594cceca908cf6b2e6fc8f1ee9d9d/README.yaml b/Simulations/057/b0e/057b0e7f9930a7ccacd6579adc12edbeb5f6eb2f/2835104546d594cceca908cf6b2e6fc8f1ee9d9d/README.yaml index 3db19ce937..b73cf0a097 100644 --- a/Simulations/057/b0e/057b0e7f9930a7ccacd6579adc12edbeb5f6eb2f/2835104546d594cceca908cf6b2e6fc8f1ee9d9d/README.yaml +++ b/Simulations/057/b0e/057b0e7f9930a7ccacd6579adc12edbeb5f6eb2f/2835104546d594cceca908cf6b2e6fc8f1ee9d9d/README.yaml @@ -48,9 +48,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 879 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (76:12:12) bilayer at 300 K (OPLS3e, GROMACS Desmond of Schrodinger 2019-4, 1000 ns) [NMRlipids simulation 879] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (76:12:12) bilayer at 300 + K (OPLS3e, GROMACS Desmond of Schrodinger 2019-4, 1000 ns) [NMRlipids simulation + 879] alternateName: POPC, 44 w/l, 300 K, 0.2 M NaCl - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 76 mol%), 32 CLA (12 mol%) and 32 SOD (12 mol%) at 300 K. Simulated with OPLS3e in GROMACS Desmond of Schrodinger 2019-4 for 1000 ns (53504 atoms). Deposited as NMRlipids Databank simulation 879 and available from https://doi.org/10.5281/zenodo.10202795. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 76 mol%), 32 CLA (12 mol%) and 32 SOD (12 mol%) at 300 K. Simulated with OPLS3e + in GROMACS Desmond of Schrodinger 2019-4 for 1000 ns (53504 atoms). Deposited + as NMRlipids Databank simulation 879 and available from https://doi.org/10.5281/zenodo.10202795. sameAs: https://doi.org/10.5281/zenodo.10202795 datePublished: '2022' license: @@ -141,7 +146,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.10202795 identifier: 10.5281/zenodo.10202795 url: https://doi.org/10.5281/zenodo.10202795 - name: MD simulation of POPC bilayer with OPLS3e force field, 200 mM NaCl part 1 + name: MD simulation of POPC bilayer with OPLS3e force field, 200 mM NaCl part + 1 publisher: Zenodo _source: api: datacite diff --git a/Simulations/06e/901/06e901200c6177b048a59247ca837bcc608758df/c243e0a0829f22a38f6d337b032db10fb366a4b0/README.yaml b/Simulations/06e/901/06e901200c6177b048a59247ca837bcc608758df/c243e0a0829f22a38f6d337b032db10fb366a4b0/README.yaml index 8b9c436c9e..49527209f9 100644 --- a/Simulations/06e/901/06e901200c6177b048a59247ca837bcc608758df/c243e0a0829f22a38f6d337b032db10fb366a4b0/README.yaml +++ b/Simulations/06e/901/06e901200c6177b048a59247ca837bcc608758df/c243e0a0829f22a38f6d337b032db10fb366a4b0/README.yaml @@ -40,9 +40,12 @@ EXPERIMENT: - 10.1016/j.bbamem.2011.07.022/4 ID: 911 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC bilayer at 322 K (CHARMM36, GROMACS, 100 ns) [NMRlipids simulation 911] + name: Molecular dynamics trajectory of a DPPC bilayer at 322 K (CHARMM36, GROMACS, + 100 ns) [NMRlipids simulation 911] alternateName: DPPC - description: Molecular dynamics trajectory of a lipid bilayer of 40 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) at 322 K. Simulated with CHARMM36 in GROMACS for 100 ns (10135 atoms). Deposited as NMRlipids Databank simulation 911 and available from https://doi.org/10.5281/zenodo.20524112. + description: Molecular dynamics trajectory of a lipid bilayer of 40 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) + at 322 K. Simulated with CHARMM36 in GROMACS for 100 ns (10135 atoms). Deposited + as NMRlipids Databank simulation 911 and available from https://doi.org/10.5281/zenodo.20524112. sameAs: https://doi.org/10.5281/zenodo.20524112 datePublished: '2026-06-04' license: @@ -138,7 +141,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.20524112 identifier: 10.5281/zenodo.20524112 url: https://doi.org/10.5281/zenodo.20524112 - name: MD simulation trajectory and related files for DPPC lipid bilayer in full hydration at 322 K + name: MD simulation trajectory and related files for DPPC lipid bilayer in full + hydration at 322 K publisher: Zenodo _source: api: datacite diff --git a/Simulations/06f/201/06f201c4956d80ad61631c22a3609537677e7b6b/8252ce028a849fbd420db6c3e53340889c0021d5/README.yaml b/Simulations/06f/201/06f201c4956d80ad61631c22a3609537677e7b6b/8252ce028a849fbd420db6c3e53340889c0021d5/README.yaml index 9f34fda5ea..1f3553c31f 100644 --- a/Simulations/06f/201/06f201c4956d80ad61631c22a3609537677e7b6b/8252ce028a849fbd420db6c3e53340889c0021d5/README.yaml +++ b/Simulations/06f/201/06f201c4956d80ad61631c22a3609537677e7b6b/8252ce028a849fbd420db6c3e53340889c0021d5/README.yaml @@ -49,9 +49,14 @@ EXPERIMENT: POPC: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a SOD/POPC/TOCL (50:25:25) bilayer at 310 K (Charmm36, GROMACS, 540 ns) [NMRlipids simulation 771] + name: Molecular dynamics trajectory of a SOD/POPC/TOCL (50:25:25) bilayer at 310 + K (Charmm36, GROMACS, 540 ns) [NMRlipids simulation 771] alternateName: POPC/TOCL mixture - description: Molecular dynamics trajectory of a lipid bilayer of 120 SOD (50 mol%), 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 25 mol%) and 60 TOCL (1’,3’-Bis[1,2-dioleoyl-sn-glycero-3-phospho]-glycerol, 25 mol%) at 310 K. Simulated with Charmm36 in GROMACS for 540 ns (59040 atoms). Deposited as NMRlipids Databank simulation 771 and available from https://doi.org/10.5281/zenodo.13984206. + description: Molecular dynamics trajectory of a lipid bilayer of 120 SOD (50 mol%), + 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 25 mol%) and 60 TOCL + (1’,3’-Bis[1,2-dioleoyl-sn-glycero-3-phospho]-glycerol, 25 mol%) at 310 K. Simulated + with Charmm36 in GROMACS for 540 ns (59040 atoms). Deposited as NMRlipids Databank + simulation 771 and available from https://doi.org/10.5281/zenodo.13984206. sameAs: https://doi.org/10.5281/zenodo.13984206 datePublished: '2023-09-19' license: diff --git a/Simulations/077/21a/07721a49841b52e375700f4828e36ddfdf4b00dd/27b4b185112cb3cfc6744dc11e0fbfb4430ecefb/README.yaml b/Simulations/077/21a/07721a49841b52e375700f4828e36ddfdf4b00dd/27b4b185112cb3cfc6744dc11e0fbfb4430ecefb/README.yaml index 9d8342e4df..828b857633 100644 --- a/Simulations/077/21a/07721a49841b52e375700f4828e36ddfdf4b00dd/27b4b185112cb3cfc6744dc11e0fbfb4430ecefb/README.yaml +++ b/Simulations/077/21a/07721a49841b52e375700f4828e36ddfdf4b00dd/27b4b185112cb3cfc6744dc11e0fbfb4430ecefb/README.yaml @@ -38,9 +38,12 @@ EXPERIMENT: - 10.1016/j.bbamem.2011.07.022/9 ID: 920 bioschema_properties: - name: Molecular dynamics trajectory of a DLPC bilayer at 333 K (CHARMM36/LJ-PME, GROMACS Gromacs 2022, 100 ns) [NMRlipids simulation 920] + name: Molecular dynamics trajectory of a DLPC bilayer at 333 K (CHARMM36/LJ-PME, + GROMACS Gromacs 2022, 100 ns) [NMRlipids simulation 920] alternateName: Fully hydrated DLPC bilayer in SPC/E water (LJ_cutoff=1.2 nm) - description: Molecular dynamics trajectory of a lipid bilayer of 100 DLPC (1,2-dilauroyl-sn-glycero-3-phosphocholine) at 333 K. Simulated with CHARMM36/LJ-PME in GROMACS Gromacs 2022 for 100 ns (23542 atoms). Deposited as NMRlipids Databank simulation 920 and available from https://doi.org/10.5281/zenodo.20579050. + description: Molecular dynamics trajectory of a lipid bilayer of 100 DLPC (1,2-dilauroyl-sn-glycero-3-phosphocholine) + at 333 K. Simulated with CHARMM36/LJ-PME in GROMACS Gromacs 2022 for 100 ns (23542 + atoms). Deposited as NMRlipids Databank simulation 920 and available from https://doi.org/10.5281/zenodo.20579050. sameAs: https://doi.org/10.5281/zenodo.20579050 datePublished: '2026-06-07' license: @@ -131,7 +134,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.20579050 identifier: 10.5281/zenodo.20579050 url: https://doi.org/10.5281/zenodo.20579050 - name: Fully hydrated DLPC bilayer at different temperatures simulated using CHARMM36 with LJ-PME and LJ-cutoff + name: Fully hydrated DLPC bilayer at different temperatures simulated using CHARMM36 + with LJ-PME and LJ-cutoff publisher: Zenodo _source: api: datacite diff --git a/Simulations/07d/cf3/07dcf38cf72985a9535571aaa39d7ae76921838b/9633603ac288bf90cb41aeac480bd1b222658439/README.yaml b/Simulations/07d/cf3/07dcf38cf72985a9535571aaa39d7ae76921838b/9633603ac288bf90cb41aeac480bd1b222658439/README.yaml index ac5c4138ac..b4241309f3 100644 --- a/Simulations/07d/cf3/07dcf38cf72985a9535571aaa39d7ae76921838b/9633603ac288bf90cb41aeac480bd1b222658439/README.yaml +++ b/Simulations/07d/cf3/07dcf38cf72985a9535571aaa39d7ae76921838b/9633603ac288bf90cb41aeac480bd1b222658439/README.yaml @@ -48,9 +48,12 @@ EXPERIMENT: - 10.1021/jp511159q/1 ID: 352 bioschema_properties: - name: Molecular dynamics trajectory of a POPE bilayer at 310 K (CHARMM36-UA, GROMACS 5.0.6, 100 ns) [NMRlipids simulation 352] + name: Molecular dynamics trajectory of a POPE bilayer at 310 K (CHARMM36-UA, GROMACS + 5.0.6, 100 ns) [NMRlipids simulation 352] alternateName: 336POPE_15254SOL_310K_v2 - description: Molecular dynamics trajectory of a lipid bilayer of 336 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) at 310 K. Simulated with CHARMM36-UA in GROMACS 5.0.6 for 100 ns (67602 atoms). Deposited as NMRlipids Databank simulation 352 and available from https://doi.org/10.5281/zenodo.1293774. + description: Molecular dynamics trajectory of a lipid bilayer of 336 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) + at 310 K. Simulated with CHARMM36-UA in GROMACS 5.0.6 for 100 ns (67602 atoms). + Deposited as NMRlipids Databank simulation 352 and available from https://doi.org/10.5281/zenodo.1293774. sameAs: https://doi.org/10.5281/zenodo.1293774 datePublished: '2018-06-20' license: @@ -140,7 +143,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1293774 identifier: 10.5281/zenodo.1293774 url: https://doi.org/10.5281/zenodo.1293774 - name: 'Charmm36-Ua Pope Simulations (Versions 1 And 2) 310 K (Note: Hexagonal Membrane And Pope Is Called Peua)' + name: 'Charmm36-Ua Pope Simulations (Versions 1 And 2) 310 K (Note: Hexagonal + Membrane And Pope Is Called Peua)' publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/085/8c4/0858c495ce10230280aaaaf94ad25f33808af61e/544e202023374bf1a834390452bbe3c727b1abf4/README.yaml b/Simulations/085/8c4/0858c495ce10230280aaaaf94ad25f33808af61e/544e202023374bf1a834390452bbe3c727b1abf4/README.yaml index 558eebb1a0..8cf3e526f9 100644 --- a/Simulations/085/8c4/0858c495ce10230280aaaaf94ad25f33808af61e/544e202023374bf1a834390452bbe3c727b1abf4/README.yaml +++ b/Simulations/085/8c4/0858c495ce10230280aaaaf94ad25f33808af61e/544e202023374bf1a834390452bbe3c727b1abf4/README.yaml @@ -55,9 +55,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 866 bioschema_properties: - name: Molecular dynamics trajectory of a NH4/POPI/POPE (38:38:25) bilayer at 310 K (CHARMM36, GROMACS 2022.4, 500 ns) [NMRlipids simulation 866] + name: Molecular dynamics trajectory of a NH4/POPI/POPE (38:38:25) bilayer at 310 + K (CHARMM36, GROMACS 2022.4, 500 ns) [NMRlipids simulation 866] alternateName: POPI-POPE (60:40), full hydration, 310 K, NH4+ counter ions - description: Molecular dynamics trajectory of a lipid bilayer of 120 NH4 (38 mol%), 120 POPI (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoinositol, 38 mol%) and 80 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 25 mol%) at 310 K. Simulated with CHARMM36 in GROMACS 2022.4 for 500 ns (57040 atoms). Deposited as NMRlipids Databank simulation 866 and available from https://doi.org/10.5281/zenodo.10260376. + description: Molecular dynamics trajectory of a lipid bilayer of 120 NH4 (38 mol%), + 120 POPI (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoinositol, 38 mol%) and 80 POPE + (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 25 mol%) at 310 K. Simulated + with CHARMM36 in GROMACS 2022.4 for 500 ns (57040 atoms). Deposited as NMRlipids + Databank simulation 866 and available from https://doi.org/10.5281/zenodo.10260376. sameAs: https://doi.org/10.5281/zenodo.10260376 datePublished: '2023-12-18' license: diff --git a/Simulations/09a/f0e/09af0e2f023dc2422896038a251fdab72b2afa8a/b38ac955449d167237a118ba64675fc0c9ad6aeb/README.yaml b/Simulations/09a/f0e/09af0e2f023dc2422896038a251fdab72b2afa8a/b38ac955449d167237a118ba64675fc0c9ad6aeb/README.yaml index 6492ff8c51..656b94264c 100644 --- a/Simulations/09a/f0e/09af0e2f023dc2422896038a251fdab72b2afa8a/b38ac955449d167237a118ba64675fc0c9ad6aeb/README.yaml +++ b/Simulations/09a/f0e/09af0e2f023dc2422896038a251fdab72b2afa8a/b38ac955449d167237a118ba64675fc0c9ad6aeb/README.yaml @@ -54,9 +54,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 611 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/CLA/SOD (82:9:9) bilayer at 323 K (Berger-DPPC-98, GROMACS 5.0.4, 120 ns) [NMRlipids simulation 611] + name: Molecular dynamics trajectory of a DPPC/CLA/SOD (82:9:9) bilayer at 323 K + (Berger-DPPC-98, GROMACS 5.0.4, 120 ns) [NMRlipids simulation 611] alternateName: 72DPPC_2864SOL_8SOD_8CLA_323K - description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 82 mol%), 8 CLA (9 mol%) and 8 SOD (9 mol%) at 323 K. Simulated with Berger-DPPC-98 in GROMACS 5.0.4 for 120 ns (12208 atoms). Deposited as NMRlipids Databank simulation 611 and available from https://doi.org/10.5281/zenodo.16320. + description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 82 mol%), 8 CLA (9 mol%) and 8 SOD (9 mol%) at 323 K. Simulated with Berger-DPPC-98 + in GROMACS 5.0.4 for 120 ns (12208 atoms). Deposited as NMRlipids Databank simulation + 611 and available from https://doi.org/10.5281/zenodo.16320. sameAs: https://doi.org/10.5281/zenodo.16320 datePublished: '2015-03-24' license: diff --git a/Simulations/09c/1d5/09c1d59682d4fe06dbc642ec00481eb6249ec26f/9827da71c5d90fcd3398b521ffa3a3fb2966afb1/README.yaml b/Simulations/09c/1d5/09c1d59682d4fe06dbc642ec00481eb6249ec26f/9827da71c5d90fcd3398b521ffa3a3fb2966afb1/README.yaml index ce333fa4d4..d291e8c37b 100644 --- a/Simulations/09c/1d5/09c1d59682d4fe06dbc642ec00481eb6249ec26f/9827da71c5d90fcd3398b521ffa3a3fb2966afb1/README.yaml +++ b/Simulations/09c/1d5/09c1d59682d4fe06dbc642ec00481eb6249ec26f/9827da71c5d90fcd3398b521ffa3a3fb2966afb1/README.yaml @@ -53,9 +53,14 @@ EXPERIMENT: TOCL: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a TMA/TOCL/CLA (65:30:5) bilayer at 303.15 K (Charmm36, GROMACS 2023.2, 500 ns) [NMRlipids simulation 826] + name: Molecular dynamics trajectory of a TMA/TOCL/CLA (65:30:5) bilayer at 303.15 + K (Charmm36, GROMACS 2023.2, 500 ns) [NMRlipids simulation 826] alternateName: TOCL_66_TMA_Cl_T303_32w/P - description: Molecular dynamics trajectory of a lipid bilayer of 143 TMA (65 mol%), 66 TOCL (1’,3’-Bis[1,2-dioleoyl-sn-glycero-3-phospho]-glycerol, 30 mol%) and 11 CLA (5 mol%) at 303.15 K. Simulated with Charmm36 in GROMACS 2023.2 for 500 ns (31578 atoms). Deposited as NMRlipids Databank simulation 826 and available from https://doi.org/10.5281/zenodo.13933145. + description: Molecular dynamics trajectory of a lipid bilayer of 143 TMA (65 mol%), + 66 TOCL (1’,3’-Bis[1,2-dioleoyl-sn-glycero-3-phospho]-glycerol, 30 mol%) and 11 + CLA (5 mol%) at 303.15 K. Simulated with Charmm36 in GROMACS 2023.2 for 500 ns + (31578 atoms). Deposited as NMRlipids Databank simulation 826 and available from + https://doi.org/10.5281/zenodo.13933145. sameAs: https://doi.org/10.5281/zenodo.13933145 datePublished: '2024-10-15' license: diff --git a/Simulations/0a2/272/0a22727a0659852772b4a1193ced99c5981fb739/973cf49703e3217f44b5c18759fd8926e8f5d1f1/README.yaml b/Simulations/0a2/272/0a22727a0659852772b4a1193ced99c5981fb739/973cf49703e3217f44b5c18759fd8926e8f5d1f1/README.yaml index 178f4bbd47..9ab8522a92 100644 --- a/Simulations/0a2/272/0a22727a0659852772b4a1193ced99c5981fb739/973cf49703e3217f44b5c18759fd8926e8f5d1f1/README.yaml +++ b/Simulations/0a2/272/0a22727a0659852772b4a1193ced99c5981fb739/973cf49703e3217f44b5c18759fd8926e8f5d1f1/README.yaml @@ -47,9 +47,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 344 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 310 K (Berger, GROMACS 3.1.4, 40 ns) [NMRlipids simulation 344] + name: Molecular dynamics trajectory of a POPC bilayer at 310 K (Berger, GROMACS + 3.1.4, 40 ns) [NMRlipids simulation 344] alternateName: POPClipidbilayer_310K_Berger - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 310 K. Simulated with Berger in GROMACS 3.1.4 for 40 ns (17621 atoms). Deposited as NMRlipids Databank simulation 344 and available from https://doi.org/10.5281/zenodo.1230170. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 310 K. Simulated with Berger in GROMACS 3.1.4 for 40 ns (17621 atoms). Deposited + as NMRlipids Databank simulation 344 and available from https://doi.org/10.5281/zenodo.1230170. sameAs: https://doi.org/10.5281/zenodo.1230170 datePublished: '2018-04-26' license: diff --git a/Simulations/0a3/34e/0a334eb7da0eb8b9132ee5052392f58587e114a3/e9dc01b944365772afa0038d1349e15b03fe4b6c/README.yaml b/Simulations/0a3/34e/0a334eb7da0eb8b9132ee5052392f58587e114a3/e9dc01b944365772afa0038d1349e15b03fe4b6c/README.yaml index 234898a2c6..a2a9e7b33e 100644 --- a/Simulations/0a3/34e/0a334eb7da0eb8b9132ee5052392f58587e114a3/e9dc01b944365772afa0038d1349e15b03fe4b6c/README.yaml +++ b/Simulations/0a3/34e/0a334eb7da0eb8b9132ee5052392f58587e114a3/e9dc01b944365772afa0038d1349e15b03fe4b6c/README.yaml @@ -50,9 +50,13 @@ SOFTWARE: gromacs DIR_WRK: /usr/home/bort/Databank ID: 245 bioschema_properties: - name: Molecular dynamics trajectory of a DOPC/CHOL (90:10) bilayer at 310 K (CHARMM36, GROMACS, 1000 ns) [NMRlipids simulation 245] + name: Molecular dynamics trajectory of a DOPC/CHOL (90:10) bilayer at 310 K (CHARMM36, + GROMACS, 1000 ns) [NMRlipids simulation 245] alternateName: 260DOPC_28CHOL_11520SOL_310K - description: Molecular dynamics trajectory of a lipid bilayer of 260 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, 90 mol%) and 28 CHOL (cholesterol, 10 mol%) at 310 K. Simulated with CHARMM36 in GROMACS for 1000 ns (72512 atoms). Deposited as NMRlipids Databank simulation 245 and available from https://doi.org/10.5281/zenodo.2653721. + description: Molecular dynamics trajectory of a lipid bilayer of 260 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, + 90 mol%) and 28 CHOL (cholesterol, 10 mol%) at 310 K. Simulated with CHARMM36 + in GROMACS for 1000 ns (72512 atoms). Deposited as NMRlipids Databank simulation + 245 and available from https://doi.org/10.5281/zenodo.2653721. sameAs: https://doi.org/10.5281/zenodo.2653721 datePublished: '2019-04-29' license: @@ -141,7 +145,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.2653721 identifier: 10.5281/zenodo.2653721 url: https://doi.org/10.5281/zenodo.2653721 - name: Atomistic simulations of cholesterol in symmetric lipid bilayers with varying degrees of lipid chain unsaturation + name: Atomistic simulations of cholesterol in symmetric lipid bilayers with varying + degrees of lipid chain unsaturation publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/0a3/3e7/0a33e7ca5e8c7a399e40936777ffa7b236154ed8/8e731b9c41f4092328aa92f73fd89f57887c3ebd/README.yaml b/Simulations/0a3/3e7/0a33e7ca5e8c7a399e40936777ffa7b236154ed8/8e731b9c41f4092328aa92f73fd89f57887c3ebd/README.yaml index 4ad3a32649..29adf4278b 100644 --- a/Simulations/0a3/3e7/0a33e7ca5e8c7a399e40936777ffa7b236154ed8/8e731b9c41f4092328aa92f73fd89f57887c3ebd/README.yaml +++ b/Simulations/0a3/3e7/0a33e7ca5e8c7a399e40936777ffa7b236154ed8/8e731b9c41f4092328aa92f73fd89f57887c3ebd/README.yaml @@ -48,9 +48,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 246 bioschema_properties: - name: Molecular dynamics trajectory of a POPE/DOG (91:9) bilayer at 310 K (Lipid17, GROMACS 18.6, 2100 ns) [NMRlipids simulation 246] + name: Molecular dynamics trajectory of a POPE/DOG (91:9) bilayer at 310 K (Lipid17, + GROMACS 18.6, 2100 ns) [NMRlipids simulation 246] alternateName: 9.4%DOGinPOPEwithLipid17 - description: Molecular dynamics trajectory of a lipid bilayer of 116 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 91 mol%) and 12 DOG (1,2-dioleoyl-sn-glycerol, 9 mol%) at 310 K. Simulated with Lipid17 in GROMACS 18.6 for 2100 ns (35092 atoms). Deposited as NMRlipids Databank simulation 246 and available from https://doi.org/10.5281/zenodo.6778072. + description: Molecular dynamics trajectory of a lipid bilayer of 116 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, + 91 mol%) and 12 DOG (1,2-dioleoyl-sn-glycerol, 9 mol%) at 310 K. Simulated with + Lipid17 in GROMACS 18.6 for 2100 ns (35092 atoms). Deposited as NMRlipids Databank + simulation 246 and available from https://doi.org/10.5281/zenodo.6778072. sameAs: https://doi.org/10.5281/zenodo.6778072 datePublished: '2022-06-29' license: diff --git a/Simulations/0a3/f01/0a3f018386b496da0c2bea395eb7fdb889f65a1c/0a3f018386b496da0c2bea395eb7fdb889f65a1c/README.yaml b/Simulations/0a3/f01/0a3f018386b496da0c2bea395eb7fdb889f65a1c/0a3f018386b496da0c2bea395eb7fdb889f65a1c/README.yaml index edf1afd7c5..e4784c7e4a 100644 --- a/Simulations/0a3/f01/0a3f018386b496da0c2bea395eb7fdb889f65a1c/0a3f018386b496da0c2bea395eb7fdb889f65a1c/README.yaml +++ b/Simulations/0a3/f01/0a3f018386b496da0c2bea395eb7fdb889f65a1c/0a3f018386b496da0c2bea395eb7fdb889f65a1c/README.yaml @@ -37,9 +37,13 @@ EXPERIMENT: - 10.1021/bi00218a003/2 FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a PILPC bilayer at 303.15 K (CHARMM36m, NAMD 3.0, 500 ns) [NMRlipids simulation 908] + name: Molecular dynamics trajectory of a PILPC bilayer at 303.15 K (CHARMM36m, NAMD + 3.0, 500 ns) [NMRlipids simulation 908] alternateName: PiLPC - description: Molecular dynamics trajectory of a lipid bilayer of 200 PILPC (1-Palmitoyl-2-isolinoleoyl phosphatidylcholine) at 303.15 K. Simulated with CHARMM36m in NAMD 3.0 for 500 ns (51600 atoms). Deposited as NMRlipids Databank simulation 908 and available from https://doi.org/10.5281/zenodo.18480411. + description: Molecular dynamics trajectory of a lipid bilayer of 200 PILPC (1-Palmitoyl-2-isolinoleoyl + phosphatidylcholine) at 303.15 K. Simulated with CHARMM36m in NAMD 3.0 for 500 + ns (51600 atoms). Deposited as NMRlipids Databank simulation 908 and available + from https://doi.org/10.5281/zenodo.18480411. sameAs: https://doi.org/10.5281/zenodo.18480411 datePublished: '2026-02-04' license: @@ -130,7 +134,9 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.18480411 identifier: 10.5281/zenodo.18480411 url: https://doi.org/10.5281/zenodo.18480411 - name: PLPC (PiLPC) lipid bilayer | 1-palmitoyl-2-isolinoleoyl-i«-glycero-3-phosphocholine with C6-C7 and the C9-C10 double bonds | 303K, CHARMM36m-WYF forcefield, NAMD 3.0.2, 2* 500 ns + name: PLPC (PiLPC) lipid bilayer | 1-palmitoyl-2-isolinoleoyl-i«-glycero-3-phosphocholine + with C6-C7 and the C9-C10 double bonds | 303K, CHARMM36m-WYF forcefield, NAMD + 3.0.2, 2* 500 ns publisher: Zenodo _source: api: datacite diff --git a/Simulations/0a4/101/0a41017641414540973e921ed22528d1f3dc414b/3c0936e61fa40cce74fd1828a2697742709e91fb/README.yaml b/Simulations/0a4/101/0a41017641414540973e921ed22528d1f3dc414b/3c0936e61fa40cce74fd1828a2697742709e91fb/README.yaml index 7b32e147c7..6a7c22622d 100644 --- a/Simulations/0a4/101/0a41017641414540973e921ed22528d1f3dc414b/3c0936e61fa40cce74fd1828a2697742709e91fb/README.yaml +++ b/Simulations/0a4/101/0a41017641414540973e921ed22528d1f3dc414b/3c0936e61fa40cce74fd1828a2697742709e91fb/README.yaml @@ -41,9 +41,12 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 334 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC bilayer at 298 K (CHARMM36, GROMACS 2016.4, 50 ns) [NMRlipids simulation 334] + name: Molecular dynamics trajectory of a DPPC bilayer at 298 K (CHARMM36, GROMACS + 2016.4, 50 ns) [NMRlipids simulation 334] alternateName: 212DPPC_29826SOL_298K - description: Molecular dynamics trajectory of a lipid bilayer of 212 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) at 298 K. Simulated with CHARMM36 in GROMACS 2016.4 for 50 ns (117038 atoms). Deposited as NMRlipids Databank simulation 334 and available from https://doi.org/10.5281/zenodo.3950029. + description: Molecular dynamics trajectory of a lipid bilayer of 212 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) + at 298 K. Simulated with CHARMM36 in GROMACS 2016.4 for 50 ns (117038 atoms). + Deposited as NMRlipids Databank simulation 334 and available from https://doi.org/10.5281/zenodo.3950029. sameAs: https://doi.org/10.5281/zenodo.3950029 datePublished: '2020-07-20' license: @@ -143,7 +146,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3950029 identifier: 10.5281/zenodo.3950029 url: https://doi.org/10.5281/zenodo.3950029 - name: 212 DPPC Molecules bilayer in pure Water, simulated at temperatures ranging from 288K to 358K + name: 212 DPPC Molecules bilayer in pure Water, simulated at temperatures ranging + from 288K to 358K publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/0b0/917/0b0917aff71a271c294c0a5aa50dc1232b2f7b19/82ff8d2baa8e6e66a638d92308cc33430a39fabb/README.yaml b/Simulations/0b0/917/0b0917aff71a271c294c0a5aa50dc1232b2f7b19/82ff8d2baa8e6e66a638d92308cc33430a39fabb/README.yaml index 3f03eff67a..da5b95ae44 100644 --- a/Simulations/0b0/917/0b0917aff71a271c294c0a5aa50dc1232b2f7b19/82ff8d2baa8e6e66a638d92308cc33430a39fabb/README.yaml +++ b/Simulations/0b0/917/0b0917aff71a271c294c0a5aa50dc1232b2f7b19/82ff8d2baa8e6e66a638d92308cc33430a39fabb/README.yaml @@ -45,9 +45,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 289 bioschema_properties: - name: Molecular dynamics trajectory of a DLPC bilayer at 300 K (Berger-DLPC-13, GROMACS 4.5.4, 80 ns) [NMRlipids simulation 289] + name: Molecular dynamics trajectory of a DLPC bilayer at 300 K (Berger-DLPC-13, + GROMACS 4.5.4, 80 ns) [NMRlipids simulation 289] alternateName: 72DLPC_864SOL_300K - description: Molecular dynamics trajectory of a lipid bilayer of 72 DLPC (1,2-dilauroyl-sn-glycero-3-phosphocholine) at 300 K. Simulated with Berger-DLPC-13 in GROMACS 4.5.4 for 80 ns (5616 atoms). Deposited as NMRlipids Databank simulation 289 and available from https://doi.org/10.5281/zenodo.16293. + description: Molecular dynamics trajectory of a lipid bilayer of 72 DLPC (1,2-dilauroyl-sn-glycero-3-phosphocholine) + at 300 K. Simulated with Berger-DLPC-13 in GROMACS 4.5.4 for 80 ns (5616 atoms). + Deposited as NMRlipids Databank simulation 289 and available from https://doi.org/10.5281/zenodo.16293. sameAs: https://doi.org/10.5281/zenodo.16293 datePublished: '2015-03-24' license: diff --git a/Simulations/0bc/296/0bc296850dd41d32a6e9aa4ac2b5dd4e84a6605f/e64b1a6ceccc9a361529be902c17c2b4b0394484/README.yaml b/Simulations/0bc/296/0bc296850dd41d32a6e9aa4ac2b5dd4e84a6605f/e64b1a6ceccc9a361529be902c17c2b4b0394484/README.yaml index 12309abbae..1feaa8673b 100644 --- a/Simulations/0bc/296/0bc296850dd41d32a6e9aa4ac2b5dd4e84a6605f/e64b1a6ceccc9a361529be902c17c2b4b0394484/README.yaml +++ b/Simulations/0bc/296/0bc296850dd41d32a6e9aa4ac2b5dd4e84a6605f/e64b1a6ceccc9a361529be902c17c2b4b0394484/README.yaml @@ -41,9 +41,12 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 244 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC bilayer at 288 K (CHARMM36, GROMACS 2016.4, 50 ns) [NMRlipids simulation 244] + name: Molecular dynamics trajectory of a DPPC bilayer at 288 K (CHARMM36, GROMACS + 2016.4, 50 ns) [NMRlipids simulation 244] alternateName: 212DPPC_29826SOL_288K - description: Molecular dynamics trajectory of a lipid bilayer of 212 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) at 288 K. Simulated with CHARMM36 in GROMACS 2016.4 for 50 ns (117038 atoms). Deposited as NMRlipids Databank simulation 244 and available from https://doi.org/10.5281/zenodo.3950029. + description: Molecular dynamics trajectory of a lipid bilayer of 212 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) + at 288 K. Simulated with CHARMM36 in GROMACS 2016.4 for 50 ns (117038 atoms). + Deposited as NMRlipids Databank simulation 244 and available from https://doi.org/10.5281/zenodo.3950029. sameAs: https://doi.org/10.5281/zenodo.3950029 datePublished: '2020-07-20' license: @@ -143,7 +146,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3950029 identifier: 10.5281/zenodo.3950029 url: https://doi.org/10.5281/zenodo.3950029 - name: 212 DPPC Molecules bilayer in pure Water, simulated at temperatures ranging from 288K to 358K + name: 212 DPPC Molecules bilayer in pure Water, simulated at temperatures ranging + from 288K to 358K publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/0bd/8bd/0bd8bd58f66c8ef8c6c5b5ba78eefcc3589775cd/2a5c22606ac14be5ab7d31bcdde4b90f04796988/README.yaml b/Simulations/0bd/8bd/0bd8bd58f66c8ef8c6c5b5ba78eefcc3589775cd/2a5c22606ac14be5ab7d31bcdde4b90f04796988/README.yaml index 9c44c3e8ca..6c1adede85 100644 --- a/Simulations/0bd/8bd/0bd8bd58f66c8ef8c6c5b5ba78eefcc3589775cd/2a5c22606ac14be5ab7d31bcdde4b90f04796988/README.yaml +++ b/Simulations/0bd/8bd/0bd8bd58f66c8ef8c6c5b5ba78eefcc3589775cd/2a5c22606ac14be5ab7d31bcdde4b90f04796988/README.yaml @@ -45,9 +45,12 @@ ID: 810 WARNINGS: PBC: z-jumps bioschema_properties: - name: Molecular dynamics trajectory of a DMPC bilayer at 314 K (OPLS4, GROMACS Desmond 2022-2, 380 ns) [NMRlipids simulation 810] + name: Molecular dynamics trajectory of a DMPC bilayer at 314 K (OPLS4, GROMACS Desmond + 2022-2, 380 ns) [NMRlipids simulation 810] alternateName: 200DMPC_2000SOL_300K - description: Molecular dynamics trajectory of a lipid bilayer of 200 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) at 314 K. Simulated with OPLS4 in GROMACS Desmond 2022-2 for 380 ns (29600 atoms). Deposited as NMRlipids Databank simulation 810 and available from https://doi.org/10.5281/zenodo.11045073. + description: Molecular dynamics trajectory of a lipid bilayer of 200 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) + at 314 K. Simulated with OPLS4 in GROMACS Desmond 2022-2 for 380 ns (29600 atoms). + Deposited as NMRlipids Databank simulation 810 and available from https://doi.org/10.5281/zenodo.11045073. sameAs: https://doi.org/10.5281/zenodo.11045073 datePublished: '2024-04-23' license: diff --git a/Simulations/0c1/7ae/0c17ae6dd0927b16739c56816c5eae34ea67a508/ba9c4e8a9bd882765db82cec67a7ab01f2504f0b/README.yaml b/Simulations/0c1/7ae/0c17ae6dd0927b16739c56816c5eae34ea67a508/ba9c4e8a9bd882765db82cec67a7ab01f2504f0b/README.yaml index 1cdbd9892e..12da020065 100644 --- a/Simulations/0c1/7ae/0c17ae6dd0927b16739c56816c5eae34ea67a508/ba9c4e8a9bd882765db82cec67a7ab01f2504f0b/README.yaml +++ b/Simulations/0c1/7ae/0c17ae6dd0927b16739c56816c5eae34ea67a508/ba9c4e8a9bd882765db82cec67a7ab01f2504f0b/README.yaml @@ -44,9 +44,12 @@ EXPERIMENT: DYPC: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a DYPC bilayer at 333.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 626] + name: Molecular dynamics trajectory of a DYPC bilayer at 333.15 K (CHARMM36, GROMACS, + 1001 ns) [NMRlipids simulation 626] alternateName: 1024DYPC_51200SOL_333K - description: Molecular dynamics trajectory of a lipid bilayer of 1024 DYPC (1,2-(16:1$^\Delta9$)-sn-glycero-3-phosphocholine) at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (282624 atoms). Deposited as NMRlipids Databank simulation 626 and available from https://doi.org/10.5281/zenodo.6943413. + description: Molecular dynamics trajectory of a lipid bilayer of 1024 DYPC (1,2-(16:1$^\Delta9$)-sn-glycero-3-phosphocholine) + at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (282624 atoms). Deposited + as NMRlipids Databank simulation 626 and available from https://doi.org/10.5281/zenodo.6943413. sameAs: https://doi.org/10.5281/zenodo.6943413 datePublished: '2022-07-30' license: @@ -134,7 +137,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.6943413 identifier: 10.5281/zenodo.6943413 url: https://doi.org/10.5281/zenodo.6943413 - name: Simulations of different single-component bilayers, three different system sizes + name: Simulations of different single-component bilayers, three different system + sizes publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/0c2/1a9/0c21a9be136ea0eb9df9e5c6cdc19f723a0af245/9ac73b6a98acb54a7a67a5d690794ad7f1e4a1d1/README.yaml b/Simulations/0c2/1a9/0c21a9be136ea0eb9df9e5c6cdc19f723a0af245/9ac73b6a98acb54a7a67a5d690794ad7f1e4a1d1/README.yaml index 0b947c211b..7b8ff89d47 100644 --- a/Simulations/0c2/1a9/0c21a9be136ea0eb9df9e5c6cdc19f723a0af245/9ac73b6a98acb54a7a67a5d690794ad7f1e4a1d1/README.yaml +++ b/Simulations/0c2/1a9/0c21a9be136ea0eb9df9e5c6cdc19f723a0af245/9ac73b6a98acb54a7a67a5d690794ad7f1e4a1d1/README.yaml @@ -46,9 +46,14 @@ TRJ: - - 100-400ns.xtc ID: 592 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPG/SOD (33:33:33) bilayer at 298 K (CHARMM36, GROMACS, 300 ns) [NMRlipids simulation 592] + name: Molecular dynamics trajectory of a POPC/POPG/SOD (33:33:33) bilayer at 298 + K (CHARMM36, GROMACS, 300 ns) [NMRlipids simulation 592] alternateName: POPC:POPG(1:1)_T298K - description: Molecular dynamics trajectory of a lipid bilayer of 150 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 33 mol%), 150 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 33 mol%) and 150 SOD (33 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for 300 ns (133800 atoms). Deposited as NMRlipids Databank simulation 592 and available from https://doi.org/10.5281/zenodo.3997116. + description: Molecular dynamics trajectory of a lipid bilayer of 150 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 33 mol%), 150 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 33 mol%) + and 150 SOD (33 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for 300 ns + (133800 atoms). Deposited as NMRlipids Databank simulation 592 and available from + https://doi.org/10.5281/zenodo.3997116. sameAs: https://doi.org/10.5281/zenodo.3997116 datePublished: '2020-08-24' license: diff --git a/Simulations/0c9/c1c/0c9c1c561dec1b86700c70f65af876256cdf06c9/acfcbedb2809e251a386740b8970b328c7c292b9/README.yaml b/Simulations/0c9/c1c/0c9c1c561dec1b86700c70f65af876256cdf06c9/acfcbedb2809e251a386740b8970b328c7c292b9/README.yaml index a0cd824aa0..0961f7f703 100644 --- a/Simulations/0c9/c1c/0c9c1c561dec1b86700c70f65af876256cdf06c9/acfcbedb2809e251a386740b8970b328c7c292b9/README.yaml +++ b/Simulations/0c9/c1c/0c9c1c561dec1b86700c70f65af876256cdf06c9/acfcbedb2809e251a386740b8970b328c7c292b9/README.yaml @@ -55,9 +55,13 @@ EXPERIMENT: POPC: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a POPC/NH4/POPI (43:29:29) bilayer at 310 K (CHARMM36, GROMACS 2022.4, 500 ns) [NMRlipids simulation 855] + name: Molecular dynamics trajectory of a POPC/NH4/POPI (43:29:29) bilayer at 310 + K (CHARMM36, GROMACS 2022.4, 500 ns) [NMRlipids simulation 855] alternateName: POPI-POPC (40:60), full hydration, 310 K, NH4+ counter ions - description: Molecular dynamics trajectory of a lipid bilayer of 120 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 43 mol%), 80 NH4 (29 mol%) and 80 POPI (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoinositol, 29 mol%) at 310 K. Simulated with CHARMM36 in GROMACS 2022.4 for 500 ns (57440 atoms). Deposited as NMRlipids Databank simulation 855 and available from https://doi.org/10.5281/zenodo.10255810. + description: Molecular dynamics trajectory of a lipid bilayer of 120 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 43 mol%), 80 NH4 (29 mol%) and 80 POPI (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoinositol, + 29 mol%) at 310 K. Simulated with CHARMM36 in GROMACS 2022.4 for 500 ns (57440 + atoms). Deposited as NMRlipids Databank simulation 855 and available from https://doi.org/10.5281/zenodo.10255810. sameAs: https://doi.org/10.5281/zenodo.10255810 datePublished: '2023-12-18' license: diff --git a/Simulations/0d3/e47/0d3e47b449cd5550a51cf78f0f0c784c9d37ae58/471a61f2450461390a127a73f120f39b0b88b567/README.yaml b/Simulations/0d3/e47/0d3e47b449cd5550a51cf78f0f0c784c9d37ae58/471a61f2450461390a127a73f120f39b0b88b567/README.yaml index 212d17be9b..86ce64cafa 100644 --- a/Simulations/0d3/e47/0d3e47b449cd5550a51cf78f0f0c784c9d37ae58/471a61f2450461390a127a73f120f39b0b88b567/README.yaml +++ b/Simulations/0d3/e47/0d3e47b449cd5550a51cf78f0f0c784c9d37ae58/471a61f2450461390a127a73f120f39b0b88b567/README.yaml @@ -45,9 +45,12 @@ EXPERIMENT: - 10.1016/j.bbamem.2011.07.022/20 ID: 356 bioschema_properties: - name: Molecular dynamics trajectory of a DMPC bilayer at 333.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 356] + name: Molecular dynamics trajectory of a DMPC bilayer at 333.15 K (CHARMM36, GROMACS, + 1001 ns) [NMRlipids simulation 356] alternateName: 1024DMPC_51200SOL_333K - description: Molecular dynamics trajectory of a lipid bilayer of 1024 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (274432 atoms). Deposited as NMRlipids Databank simulation 356 and available from https://doi.org/10.5281/zenodo.6943413. + description: Molecular dynamics trajectory of a lipid bilayer of 1024 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) + at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (274432 atoms). Deposited + as NMRlipids Databank simulation 356 and available from https://doi.org/10.5281/zenodo.6943413. sameAs: https://doi.org/10.5281/zenodo.6943413 datePublished: '2022-07-30' license: @@ -137,7 +140,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.6943413 identifier: 10.5281/zenodo.6943413 url: https://doi.org/10.5281/zenodo.6943413 - name: Simulations of different single-component bilayers, three different system sizes + name: Simulations of different single-component bilayers, three different system + sizes publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/0d5/d1d/0d5d1dcb43e775faf4e53c4f9ff255a67481bd38/9b487701b24d3fad83991e311188b08d3d5ea768/README.yaml b/Simulations/0d5/d1d/0d5d1dcb43e775faf4e53c4f9ff255a67481bd38/9b487701b24d3fad83991e311188b08d3d5ea768/README.yaml index d81d04293b..1796aa98de 100644 --- a/Simulations/0d5/d1d/0d5d1dcb43e775faf4e53c4f9ff255a67481bd38/9b487701b24d3fad83991e311188b08d3d5ea768/README.yaml +++ b/Simulations/0d5/d1d/0d5d1dcb43e775faf4e53c4f9ff255a67481bd38/9b487701b24d3fad83991e311188b08d3d5ea768/README.yaml @@ -40,9 +40,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 284 bioschema_properties: - name: Molecular dynamics trajectory of a POPG/POT (50:50) bilayer at 298 K (CHARMM36, GROMACS, 100 ns) [NMRlipids simulation 284] + name: Molecular dynamics trajectory of a POPG/POT (50:50) bilayer at 298 K (CHARMM36, + GROMACS, 100 ns) [NMRlipids simulation 284] alternateName: POPG_T298K - description: Molecular dynamics trajectory of a lipid bilayer of 118 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 50 mol%) and 118 POT (50 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for 100 ns (27434 atoms). Deposited as NMRlipids Databank simulation 284 and available from https://doi.org/10.5281/zenodo.1011096. + description: Molecular dynamics trajectory of a lipid bilayer of 118 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, + 50 mol%) and 118 POT (50 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for + 100 ns (27434 atoms). Deposited as NMRlipids Databank simulation 284 and available + from https://doi.org/10.5281/zenodo.1011096. sameAs: https://doi.org/10.5281/zenodo.1011096 datePublished: '2017-10-13' license: @@ -128,7 +132,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1011096 identifier: 10.5281/zenodo.1011096 url: https://doi.org/10.5281/zenodo.1011096 - name: Popg Lipid Bilayer Simulation At T298K Ran With Model_Charmm_Gui Force Field And Gromacs + name: Popg Lipid Bilayer Simulation At T298K Ran With Model_Charmm_Gui Force Field + And Gromacs publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/0e9/f5e/0e9f5e64ad7244273eb2f544966ba7dd606fbbb1/2578273ee378997849b0bec8b8b3414797cdce73/README.yaml b/Simulations/0e9/f5e/0e9f5e64ad7244273eb2f544966ba7dd606fbbb1/2578273ee378997849b0bec8b8b3414797cdce73/README.yaml index 852417bbee..69feff4033 100644 --- a/Simulations/0e9/f5e/0e9f5e64ad7244273eb2f544966ba7dd606fbbb1/2578273ee378997849b0bec8b8b3414797cdce73/README.yaml +++ b/Simulations/0e9/f5e/0e9f5e64ad7244273eb2f544966ba7dd606fbbb1/2578273ee378997849b0bec8b8b3414797cdce73/README.yaml @@ -50,9 +50,13 @@ WARNINGS: PBC: z-jumps ID: 490 bioschema_properties: - name: Molecular dynamics trajectory of a CHOL/POPC (59:41) bilayer at 303 K (Lipid14, GROMACS 5.0.4, 200 ns) [NMRlipids simulation 490] + name: Molecular dynamics trajectory of a CHOL/POPC (59:41) bilayer at 303 K (Lipid14, + GROMACS 5.0.4, 200 ns) [NMRlipids simulation 490] alternateName: 52POPC_76CHOL_3968SOL_303K - description: Molecular dynamics trajectory of a lipid bilayer of 76 CHOL (cholesterol, 59 mol%) and 52 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 41 mol%) at 303 K. Simulated with Lipid14 in GROMACS 5.0.4 for 200 ns (24496 atoms). Deposited as NMRlipids Databank simulation 490 and available from https://doi.org/10.5281/zenodo.3871008. + description: Molecular dynamics trajectory of a lipid bilayer of 76 CHOL (cholesterol, + 59 mol%) and 52 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 41 mol%) + at 303 K. Simulated with Lipid14 in GROMACS 5.0.4 for 200 ns (24496 atoms). Deposited + as NMRlipids Databank simulation 490 and available from https://doi.org/10.5281/zenodo.3871008. sameAs: https://doi.org/10.5281/zenodo.3871008 datePublished: '2020-06-01' license: @@ -141,7 +145,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3871008 identifier: 10.5281/zenodo.3871008 url: https://doi.org/10.5281/zenodo.3871008 - name: 'MD simulations of bilayers containing POPC and Cholesterol: 52POPC_76CHL_31Nwat_neutral (lipid14)' + name: 'MD simulations of bilayers containing POPC and Cholesterol: 52POPC_76CHL_31Nwat_neutral + (lipid14)' publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/0eb/897/0eb897008bf6afbda2423b4ffe10f556d0d31a61/3966b2db2052ef1ac31886ff65c428112a7a1970/README.yaml b/Simulations/0eb/897/0eb897008bf6afbda2423b4ffe10f556d0d31a61/3966b2db2052ef1ac31886ff65c428112a7a1970/README.yaml index 7c5911d82b..51028b561f 100644 --- a/Simulations/0eb/897/0eb897008bf6afbda2423b4ffe10f556d0d31a61/3966b2db2052ef1ac31886ff65c428112a7a1970/README.yaml +++ b/Simulations/0eb/897/0eb897008bf6afbda2423b4ffe10f556d0d31a61/3966b2db2052ef1ac31886ff65c428112a7a1970/README.yaml @@ -33,9 +33,12 @@ EXPERIMENT: DPPC: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a DPPC bilayer at 333 K (CHARMM36, GROMACS, 100 ns) [NMRlipids simulation 890] + name: Molecular dynamics trajectory of a DPPC bilayer at 333 K (CHARMM36, GROMACS, + 100 ns) [NMRlipids simulation 890] alternateName: DPPC - description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) at 333 K. Simulated with CHARMM36 in GROMACS for 100 ns (13347 atoms). Deposited as NMRlipids Databank simulation 890 and available from https://doi.org/10.5281/zenodo.7572990. + description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) + at 333 K. Simulated with CHARMM36 in GROMACS for 100 ns (13347 atoms). Deposited + as NMRlipids Databank simulation 890 and available from https://doi.org/10.5281/zenodo.7572990. sameAs: https://doi.org/10.5281/zenodo.7572990 datePublished: '2023-01-26' license: @@ -125,7 +128,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.7572990 identifier: 10.5281/zenodo.7572990 url: https://doi.org/10.5281/zenodo.7572990 - name: 'MD simulation input files and results for ,,Atomistic MD simulations of n-alkanes in a phospholipid bilayer: CHARMM36 versus Slipids"' + name: 'MD simulation input files and results for ,,Atomistic MD simulations of + n-alkanes in a phospholipid bilayer: CHARMM36 versus Slipids"' publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/0ee/05e/0ee05e1e79df817550a61e81325640721a390b8c/9bff2a04f58c3e886cee2ee1ab30c056d1fc9393/README.yaml b/Simulations/0ee/05e/0ee05e1e79df817550a61e81325640721a390b8c/9bff2a04f58c3e886cee2ee1ab30c056d1fc9393/README.yaml index 9d4c15eca6..6ef657634c 100644 --- a/Simulations/0ee/05e/0ee05e1e79df817550a61e81325640721a390b8c/9bff2a04f58c3e886cee2ee1ab30c056d1fc9393/README.yaml +++ b/Simulations/0ee/05e/0ee05e1e79df817550a61e81325640721a390b8c/9bff2a04f58c3e886cee2ee1ab30c056d1fc9393/README.yaml @@ -49,9 +49,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 552 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (70:30) bilayer at 310.15 K (CHARMM36, GROMACS 5.0, 500 ns) [NMRlipids simulation 552] + name: Molecular dynamics trajectory of a POPC/CHOL (70:30) bilayer at 310.15 K (CHARMM36, + GROMACS 5.0, 500 ns) [NMRlipids simulation 552] alternateName: 86CHOL_200POPC_9000SOL_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 70 mol%) and 86 CHOL (cholesterol, 30 mol%) at 310.15 K. Simulated with CHARMM36 in GROMACS 5.0 for 500 ns (60164 atoms). Deposited as NMRlipids Databank simulation 552 and available from https://doi.org/10.5281/zenodo.3237420. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 70 mol%) and 86 CHOL (cholesterol, 30 mol%) at 310.15 K. Simulated with CHARMM36 + in GROMACS 5.0 for 500 ns (60164 atoms). Deposited as NMRlipids Databank simulation + 552 and available from https://doi.org/10.5281/zenodo.3237420. sameAs: https://doi.org/10.5281/zenodo.3237420 datePublished: '2016-10-09' license: @@ -140,7 +144,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3237420 identifier: 10.5281/zenodo.3237420 url: https://doi.org/10.5281/zenodo.3237420 - name: POPC with 0, 10, 20, and 30 mol-% of cholesterol at 310 K. Charmm36 force field. + name: POPC with 0, 10, 20, and 30 mol-% of cholesterol at 310 K. Charmm36 force + field. publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/0f2/d02/0f2d02d844c1290ae8e9b058d19e92065e71dd06/a5d989590567888284ba4d86b1cfe674af0f8c19/README.yaml b/Simulations/0f2/d02/0f2d02d844c1290ae8e9b058d19e92065e71dd06/a5d989590567888284ba4d86b1cfe674af0f8c19/README.yaml index 4a864ee278..5841907ae3 100644 --- a/Simulations/0f2/d02/0f2d02d844c1290ae8e9b058d19e92065e71dd06/a5d989590567888284ba4d86b1cfe674af0f8c19/README.yaml +++ b/Simulations/0f2/d02/0f2d02d844c1290ae8e9b058d19e92065e71dd06/a5d989590567888284ba4d86b1cfe674af0f8c19/README.yaml @@ -48,9 +48,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 507 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (64:18:18) bilayer at 298 K (MacRog, GROMACS 4.5, 50 ns) [NMRlipids simulation 507] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (64:18:18) bilayer at 298 + K (MacRog, GROMACS 4.5, 50 ns) [NMRlipids simulation 507] alternateName: 288POPC_14446SOL_81SOD_81CLA_298K - description: Molecular dynamics trajectory of a lipid bilayer of 288 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 64 mol%), 81 CLA (18 mol%) and 81 SOD (18 mol%) at 298 K. Simulated with MacRog in GROMACS 4.5 for 50 ns (82092 atoms). Deposited as NMRlipids Databank simulation 507 and available from https://doi.org/10.5281/zenodo.14976. + description: Molecular dynamics trajectory of a lipid bilayer of 288 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 64 mol%), 81 CLA (18 mol%) and 81 SOD (18 mol%) at 298 K. Simulated with MacRog + in GROMACS 4.5 for 50 ns (82092 atoms). Deposited as NMRlipids Databank simulation + 507 and available from https://doi.org/10.5281/zenodo.14976. sameAs: https://doi.org/10.5281/zenodo.14976 datePublished: '2015-02-10' license: diff --git a/Simulations/102/dfa/102dfa390326acd775347b1d703ccfa85e033cd8/1ad80d5d253e861f01d8f16e0d1590c6ef962916/README.yaml b/Simulations/102/dfa/102dfa390326acd775347b1d703ccfa85e033cd8/1ad80d5d253e861f01d8f16e0d1590c6ef962916/README.yaml index 71d85605aa..1cbfb345a6 100644 --- a/Simulations/102/dfa/102dfa390326acd775347b1d703ccfa85e033cd8/1ad80d5d253e861f01d8f16e0d1590c6ef962916/README.yaml +++ b/Simulations/102/dfa/102dfa390326acd775347b1d703ccfa85e033cd8/1ad80d5d253e861f01d8f16e0d1590c6ef962916/README.yaml @@ -40,9 +40,12 @@ TRJ: - - prottraj.xtc ID: 151 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 303 K (Berger, GROMACS Gpu_version_2020.1, 1200 ns) [NMRlipids simulation 151] + name: Molecular dynamics trajectory of a POPC bilayer at 303 K (Berger, GROMACS + Gpu_version_2020.1, 1200 ns) [NMRlipids simulation 151] alternateName: Berger_POPC_T303K - description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 303 K. Simulated with Berger in GROMACS Gpu_version_2020.1 for 1200 ns (65330 atoms). Deposited as NMRlipids Databank simulation 151 and available from https://doi.org/10.5281/zenodo.4537207. + description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 303 K. Simulated with Berger in GROMACS Gpu_version_2020.1 for 1200 ns (65330 + atoms). Deposited as NMRlipids Databank simulation 151 and available from https://doi.org/10.5281/zenodo.4537207. sameAs: https://doi.org/10.5281/zenodo.4537207 datePublished: '2021-02-12' license: diff --git a/Simulations/107/7fb/1077fb2bdc91269d2c3e5c22f5560d62ca0901d1/23fdf201323693d01eedcd67d30a1caf11239e33/README.yaml b/Simulations/107/7fb/1077fb2bdc91269d2c3e5c22f5560d62ca0901d1/23fdf201323693d01eedcd67d30a1caf11239e33/README.yaml index b2752c8b2f..adb122dbc7 100644 --- a/Simulations/107/7fb/1077fb2bdc91269d2c3e5c22f5560d62ca0901d1/23fdf201323693d01eedcd67d30a1caf11239e33/README.yaml +++ b/Simulations/107/7fb/1077fb2bdc91269d2c3e5c22f5560d62ca0901d1/23fdf201323693d01eedcd67d30a1caf11239e33/README.yaml @@ -56,9 +56,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 496 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POT/CLA/POPS (47:26:17:9) bilayer at 298 K (CHARMM36, GROMACS, 150 ns) [NMRlipids simulation 496] + name: Molecular dynamics trajectory of a POPC/POT/CLA/POPS (47:26:17:9) bilayer + at 298 K (CHARMM36, GROMACS, 150 ns) [NMRlipids simulation 496] alternateName: 110POPC_22POPS_4929SOL_62POT_40CLA_298K - description: Molecular dynamics trajectory of a lipid bilayer of 110 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 47 mol%), 62 POT (26 mol%), 40 CLA (17 mol%) and 22 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 9 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for 150 ns (32423 atoms). Deposited as NMRlipids Databank simulation 496 and available from https://doi.org/10.5281/zenodo.1493241. + description: Molecular dynamics trajectory of a lipid bilayer of 110 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 47 mol%), 62 POT (26 mol%), 40 CLA (17 mol%) and 22 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, + 9 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for 150 ns (32423 atoms). + Deposited as NMRlipids Databank simulation 496 and available from https://doi.org/10.5281/zenodo.1493241. sameAs: https://doi.org/10.5281/zenodo.1493241 datePublished: '2018-11-21' license: diff --git a/Simulations/10c/727/10c727d1f06ad18d5a0676014c67fce3b3a4131d/3872a01e1e1fdd5d211474a565fcd9b11830e372/README.yaml b/Simulations/10c/727/10c727d1f06ad18d5a0676014c67fce3b3a4131d/3872a01e1e1fdd5d211474a565fcd9b11830e372/README.yaml index 0362ae3229..6a90bb171f 100644 --- a/Simulations/10c/727/10c727d1f06ad18d5a0676014c67fce3b3a4131d/3872a01e1e1fdd5d211474a565fcd9b11830e372/README.yaml +++ b/Simulations/10c/727/10c727d1f06ad18d5a0676014c67fce3b3a4131d/3872a01e1e1fdd5d211474a565fcd9b11830e372/README.yaml @@ -51,9 +51,13 @@ EXPERIMENT: CHOL: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a DOPC/CHOL (71:29) bilayer at 333.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 649] + name: Molecular dynamics trajectory of a DOPC/CHOL (71:29) bilayer at 333.15 K (CHARMM36, + GROMACS, 1001 ns) [NMRlipids simulation 649] alternateName: 1024DOPC_416CHOL_72000SOL_333K - description: Molecular dynamics trajectory of a lipid bilayer of 1024 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, 71 mol%) and 416 CHOL (cholesterol, 29 mol%) at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (388096 atoms). Deposited as NMRlipids Databank simulation 649 and available from https://doi.org/10.5281/zenodo.6943929. + description: Molecular dynamics trajectory of a lipid bilayer of 1024 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, + 71 mol%) and 416 CHOL (cholesterol, 29 mol%) at 333.15 K. Simulated with CHARMM36 + in GROMACS for 1001 ns (388096 atoms). Deposited as NMRlipids Databank simulation + 649 and available from https://doi.org/10.5281/zenodo.6943929. sameAs: https://doi.org/10.5281/zenodo.6943929 datePublished: '2022-07-30' license: diff --git a/Simulations/10d/2b3/10d2b34e50466845d3a5d93f8e0100b9d52b0daa/b82c05f290ec7762b7bd1611203ac0300e26d706/README.yaml b/Simulations/10d/2b3/10d2b34e50466845d3a5d93f8e0100b9d52b0daa/b82c05f290ec7762b7bd1611203ac0300e26d706/README.yaml index dc0792dd00..a3cab47bd5 100644 --- a/Simulations/10d/2b3/10d2b34e50466845d3a5d93f8e0100b9d52b0daa/b82c05f290ec7762b7bd1611203ac0300e26d706/README.yaml +++ b/Simulations/10d/2b3/10d2b34e50466845d3a5d93f8e0100b9d52b0daa/b82c05f290ec7762b7bd1611203ac0300e26d706/README.yaml @@ -55,9 +55,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 478 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (44:37:19) bilayer at 313 K (ECC-lipids, GROMACS 5.1.4, 100 ns) [NMRlipids simulation 478] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (44:37:19) bilayer at 313 + K (ECC-lipids, GROMACS 5.1.4, 100 ns) [NMRlipids simulation 478] alternateName: 128POPC_6400SOL_54CAL_108CLA_313K_OPC3model - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 44 mol%), 108 CLA (37 mol%) and 54 CAL (19 mol%) at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 100 ns (36514 atoms). Deposited as NMRlipids Databank simulation 478 and available from https://doi.org/10.5281/zenodo.1118980. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 44 mol%), 108 CLA (37 mol%) and 54 CAL (19 mol%) at 313 K. Simulated with ECC-lipids + in GROMACS 5.1.4 for 100 ns (36514 atoms). Deposited as NMRlipids Databank simulation + 478 and available from https://doi.org/10.5281/zenodo.1118980. sameAs: https://doi.org/10.5281/zenodo.1118980 datePublished: '2017-12-19' license: @@ -147,7 +151,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1118980 identifier: 10.5281/zenodo.1118980 url: https://doi.org/10.5281/zenodo.1118980 - name: Simulations Of Popc Lipid Bilayer In Water Solution At Various Nacl And Cacl2 Concentrations Using Ecc-Popc Force Field And Various Water Models + name: Simulations Of Popc Lipid Bilayer In Water Solution At Various Nacl And + Cacl2 Concentrations Using Ecc-Popc Force Field And Various Water Models publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/114/cc9/114cc9ae4f4b01297f994c101dd9a51bbe31b2ac/d09e087de242ec64b3d024b8c4e087f4f8cc2022/README.yaml b/Simulations/114/cc9/114cc9ae4f4b01297f994c101dd9a51bbe31b2ac/d09e087de242ec64b3d024b8c4e087f4f8cc2022/README.yaml index 8b19abf95d..2a4cb178b8 100644 --- a/Simulations/114/cc9/114cc9ae4f4b01297f994c101dd9a51bbe31b2ac/d09e087de242ec64b3d024b8c4e087f4f8cc2022/README.yaml +++ b/Simulations/114/cc9/114cc9ae4f4b01297f994c101dd9a51bbe31b2ac/d09e087de242ec64b3d024b8c4e087f4f8cc2022/README.yaml @@ -44,9 +44,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 482 bioschema_properties: - name: Molecular dynamics trajectory of a POPE bilayer at 313 K (GROMOS-CKP, GROMACS 5.0.6, 400 ns) [NMRlipids simulation 482] + name: Molecular dynamics trajectory of a POPE bilayer at 313 K (GROMOS-CKP, GROMACS + 5.0.6, 400 ns) [NMRlipids simulation 482] alternateName: 128POPE_3552SOL_313K_GROMOS-CKP_v2 - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) at 313 K. Simulated with GROMOS-CKP in GROMACS 5.0.6 for 400 ns (17312 atoms). Deposited as NMRlipids Databank simulation 482 and available from https://doi.org/10.5281/zenodo.1293932. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) + at 313 K. Simulated with GROMOS-CKP in GROMACS 5.0.6 for 400 ns (17312 atoms). + Deposited as NMRlipids Databank simulation 482 and available from https://doi.org/10.5281/zenodo.1293932. sameAs: https://doi.org/10.5281/zenodo.1293932 datePublished: '2018-06-20' license: diff --git a/Simulations/116/9a0/1169a0f959c9caac1671425c8ae4cd6e255dc49f/e0dbaa355f6b5faeeef73dd79514eb8364492a88/README.yaml b/Simulations/116/9a0/1169a0f959c9caac1671425c8ae4cd6e255dc49f/e0dbaa355f6b5faeeef73dd79514eb8364492a88/README.yaml index 09eae793a5..9e656b3c28 100644 --- a/Simulations/116/9a0/1169a0f959c9caac1671425c8ae4cd6e255dc49f/e0dbaa355f6b5faeeef73dd79514eb8364492a88/README.yaml +++ b/Simulations/116/9a0/1169a0f959c9caac1671425c8ae4cd6e255dc49f/e0dbaa355f6b5faeeef73dd79514eb8364492a88/README.yaml @@ -44,9 +44,14 @@ SOFTWARE: gromacs DIR_WRK: /usr/home/bort/Databank ID: 171 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC bilayer at 325 K (CHARMM36 (center of mass removed independently for upper leaflet, lower leaflet and water+ions), GROMACS 5.0.4, 500 ns) [NMRlipids simulation 171] + name: Molecular dynamics trajectory of a DPPC bilayer at 325 K (CHARMM36 (center + of mass removed independently for upper leaflet, lower leaflet and water+ions), + GROMACS 5.0.4, 500 ns) [NMRlipids simulation 171] alternateName: 72DPPC_2880SOL_325K_rmcomm_leaflets - description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) at 325 K. Simulated with CHARMM36 (center of mass removed independently for upper leaflet, lower leaflet and water+ions) in GROMACS 5.0.4 for 500 ns (18000 atoms). Deposited as NMRlipids Databank simulation 171 and available from https://doi.org/10.5281/zenodo.1009607. + description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) + at 325 K. Simulated with CHARMM36 (center of mass removed independently for upper + leaflet, lower leaflet and water+ions) in GROMACS 5.0.4 for 500 ns (18000 atoms). + Deposited as NMRlipids Databank simulation 171 and available from https://doi.org/10.5281/zenodo.1009607. sameAs: https://doi.org/10.5281/zenodo.1009607 datePublished: '2017-10-12' license: @@ -99,7 +104,8 @@ bioschema_properties: inDefinedTermSet: http://edamontology.org url: http://edamontology.org/operation_2476 - Molecular dynamics simulation (gromacs 5.0.4) - - CHARMM36 (center of mass removed independently for upper leaflet, lower leaflet and water+ions) force field + - CHARMM36 (center of mass removed independently for upper leaflet, lower leaflet + and water+ions) force field variableMeasured: - '@type': PropertyValue name: area per lipid @@ -141,7 +147,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1009607 identifier: 10.5281/zenodo.1009607 url: https://doi.org/10.5281/zenodo.1009607 - name: Set Simulations Small Pure Bilayers (72 Lipids) Using Charmm36 Ff In Gromacs (Dppc, Popc) + name: Set Simulations Small Pure Bilayers (72 Lipids) Using Charmm36 Ff In Gromacs + (Dppc, Popc) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/118/63c/11863cc69a9981c131cf84c5c0a9b0e121d4fd82/7460bf1dfb99b7838374837e35ccca3c416a7659/README.yaml b/Simulations/118/63c/11863cc69a9981c131cf84c5c0a9b0e121d4fd82/7460bf1dfb99b7838374837e35ccca3c416a7659/README.yaml index a56da8a58a..9b0ef81859 100644 --- a/Simulations/118/63c/11863cc69a9981c131cf84c5c0a9b0e121d4fd82/7460bf1dfb99b7838374837e35ccca3c416a7659/README.yaml +++ b/Simulations/118/63c/11863cc69a9981c131cf84c5c0a9b0e121d4fd82/7460bf1dfb99b7838374837e35ccca3c416a7659/README.yaml @@ -49,9 +49,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 291 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (80:20) bilayer at 310.15 K (CHARMM36, GROMACS 5.0, 500 ns) [NMRlipids simulation 291] + name: Molecular dynamics trajectory of a POPC/CHOL (80:20) bilayer at 310.15 K (CHARMM36, + GROMACS 5.0, 500 ns) [NMRlipids simulation 291] alternateName: 50CHOL_200POPC_9000SOL_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 80 mol%) and 50 CHOL (cholesterol, 20 mol%) at 310.15 K. Simulated with CHARMM36 in GROMACS 5.0 for 500 ns (57500 atoms). Deposited as NMRlipids Databank simulation 291 and available from https://doi.org/10.5281/zenodo.3237420. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 80 mol%) and 50 CHOL (cholesterol, 20 mol%) at 310.15 K. Simulated with CHARMM36 + in GROMACS 5.0 for 500 ns (57500 atoms). Deposited as NMRlipids Databank simulation + 291 and available from https://doi.org/10.5281/zenodo.3237420. sameAs: https://doi.org/10.5281/zenodo.3237420 datePublished: '2016-10-09' license: @@ -140,7 +144,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3237420 identifier: 10.5281/zenodo.3237420 url: https://doi.org/10.5281/zenodo.3237420 - name: POPC with 0, 10, 20, and 30 mol-% of cholesterol at 310 K. Charmm36 force field. + name: POPC with 0, 10, 20, and 30 mol-% of cholesterol at 310 K. Charmm36 force + field. publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/11b/f25/11bf25200b3b2fce812c817016d05acd184d9714/57f2ed2239220503b5ad88f179c49a3aa850509b/README.yaml b/Simulations/11b/f25/11bf25200b3b2fce812c817016d05acd184d9714/57f2ed2239220503b5ad88f179c49a3aa850509b/README.yaml index 52924c2428..0610a394e0 100644 --- a/Simulations/11b/f25/11bf25200b3b2fce812c817016d05acd184d9714/57f2ed2239220503b5ad88f179c49a3aa850509b/README.yaml +++ b/Simulations/11b/f25/11bf25200b3b2fce812c817016d05acd184d9714/57f2ed2239220503b5ad88f179c49a3aa850509b/README.yaml @@ -48,9 +48,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 574 bioschema_properties: - name: Molecular dynamics trajectory of a DOPS/SOD (50:50) bilayer at 303 K (GROMOS-CKP, Berger/Chiu NH3 charges and PME, GROMACS, 100 ns) [NMRlipids simulation 574] + name: Molecular dynamics trajectory of a DOPS/SOD (50:50) bilayer at 303 K (GROMOS-CKP, + Berger/Chiu NH3 charges and PME, GROMACS, 100 ns) [NMRlipids simulation 574] alternateName: 128DOPS_4480SOL_128SOD_303K_GROMOS-CKP_v2 - description: Molecular dynamics trajectory of a lipid bilayer of 128 DOPS (1,2-dioleoyl-sn-glycero-3-phospho-L-serine, 50 mol%) and 128 SOD (50 mol%) at 303 K. Simulated with GROMOS-CKP, Berger/Chiu NH3 charges and PME in GROMACS for 100 ns (20864 atoms). Deposited as NMRlipids Databank simulation 574 and available from https://doi.org/10.5281/zenodo.1129429. + description: Molecular dynamics trajectory of a lipid bilayer of 128 DOPS (1,2-dioleoyl-sn-glycero-3-phospho-L-serine, + 50 mol%) and 128 SOD (50 mol%) at 303 K. Simulated with GROMOS-CKP, Berger/Chiu + NH3 charges and PME in GROMACS for 100 ns (20864 atoms). Deposited as NMRlipids + Databank simulation 574 and available from https://doi.org/10.5281/zenodo.1129429. sameAs: https://doi.org/10.5281/zenodo.1129429 datePublished: '2017-12-24' license: @@ -139,7 +143,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1129429 identifier: 10.5281/zenodo.1129429 url: https://doi.org/10.5281/zenodo.1129429 - name: Gromos-Ckp Dops Simulations (Versions 1 And 2) 303 K With Berger/Chiu Nh3 Charges And Pme + name: Gromos-Ckp Dops Simulations (Versions 1 And 2) 303 K With Berger/Chiu Nh3 + Charges And Pme publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/124/2ab/1242ab3b5081e9e2d763827d52aa2f9485f13590/f42d633f325a1c64c75f16910c3276212a790270/README.yaml b/Simulations/124/2ab/1242ab3b5081e9e2d763827d52aa2f9485f13590/f42d633f325a1c64c75f16910c3276212a790270/README.yaml index db9ecf9b25..c7de9295bb 100644 --- a/Simulations/124/2ab/1242ab3b5081e9e2d763827d52aa2f9485f13590/f42d633f325a1c64c75f16910c3276212a790270/README.yaml +++ b/Simulations/124/2ab/1242ab3b5081e9e2d763827d52aa2f9485f13590/f42d633f325a1c64c75f16910c3276212a790270/README.yaml @@ -45,9 +45,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 804 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 300 K (OPLS4, GROMACS Desmond 2022-2, 450 ns) [NMRlipids simulation 804] + name: Molecular dynamics trajectory of a POPC bilayer at 300 K (OPLS4, GROMACS Desmond + 2022-2, 450 ns) [NMRlipids simulation 804] alternateName: 200POPC_2400SOL_300K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 300 K. Simulated with OPLS4 in GROMACS Desmond 2022-2 for 450 ns (34000 atoms). Deposited as NMRlipids Databank simulation 804 and available from https://doi.org/10.5281/zenodo.10931212. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 300 K. Simulated with OPLS4 in GROMACS Desmond 2022-2 for 450 ns (34000 atoms). + Deposited as NMRlipids Databank simulation 804 and available from https://doi.org/10.5281/zenodo.10931212. sameAs: https://doi.org/10.5281/zenodo.10931212 datePublished: '2024-04-05' license: diff --git a/Simulations/12a/1ec/12a1ecac877f46809c4377d1e8fb72977396ad94/6149c1c887124543c661efab6619943bf59e7de5/README.yaml b/Simulations/12a/1ec/12a1ecac877f46809c4377d1e8fb72977396ad94/6149c1c887124543c661efab6619943bf59e7de5/README.yaml index 14889b3751..5b9392ac82 100644 --- a/Simulations/12a/1ec/12a1ecac877f46809c4377d1e8fb72977396ad94/6149c1c887124543c661efab6619943bf59e7de5/README.yaml +++ b/Simulations/12a/1ec/12a1ecac877f46809c4377d1e8fb72977396ad94/6149c1c887124543c661efab6619943bf59e7de5/README.yaml @@ -53,9 +53,13 @@ EXPERIMENT: - 10.1039/C4SM00066H/3 ID: 521 bioschema_properties: - name: Molecular dynamics trajectory of a POPS/SOD (50:50) bilayer at 298 K (Lipid17 and ff99 ions, GROMACS 2018.0, 1000 ns) [NMRlipids simulation 521] + name: Molecular dynamics trajectory of a POPS/SOD (50:50) bilayer at 298 K (Lipid17 + and ff99 ions, GROMACS 2018.0, 1000 ns) [NMRlipids simulation 521] alternateName: 72POPS_3600SOL_72SOD_298K - description: Molecular dynamics trajectory of a lipid bilayer of 72 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 50 mol%) and 72 SOD (50 mol%) at 298 K. Simulated with Lipid17 and ff99 ions in GROMACS 2018.0 for 1000 ns (20016 atoms). Deposited as NMRlipids Databank simulation 521 and available from https://doi.org/10.5281/zenodo.1487906. + description: Molecular dynamics trajectory of a lipid bilayer of 72 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, + 50 mol%) and 72 SOD (50 mol%) at 298 K. Simulated with Lipid17 and ff99 ions in + GROMACS 2018.0 for 1000 ns (20016 atoms). Deposited as NMRlipids Databank simulation + 521 and available from https://doi.org/10.5281/zenodo.1487906. sameAs: https://doi.org/10.5281/zenodo.1487906 datePublished: '2018-11-14' license: @@ -150,7 +154,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1487906 identifier: 10.5281/zenodo.1487906 url: https://doi.org/10.5281/zenodo.1487906 - name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS with the lipid17 force field and ff99 ions + name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS + with the lipid17 force field and ff99 ions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/12e/fee/12efeef315c1170e422ed54450183e1b66b85485/3e707ddef01e5b1056299393f72cb65e3436fc15/README.yaml b/Simulations/12e/fee/12efeef315c1170e422ed54450183e1b66b85485/3e707ddef01e5b1056299393f72cb65e3436fc15/README.yaml index 6e1ba26aec..21c249be70 100644 --- a/Simulations/12e/fee/12efeef315c1170e422ed54450183e1b66b85485/3e707ddef01e5b1056299393f72cb65e3436fc15/README.yaml +++ b/Simulations/12e/fee/12efeef315c1170e422ed54450183e1b66b85485/3e707ddef01e5b1056299393f72cb65e3436fc15/README.yaml @@ -53,9 +53,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/8 ID: 550 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (62:38) bilayer at 298.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 550] + name: Molecular dynamics trajectory of a POPC/CHOL (62:38) bilayer at 298.15 K (CHARMM36, + GROMACS, 1001 ns) [NMRlipids simulation 550] alternateName: 1024POPC_640CHOL_83200SOL_298K - description: Molecular dynamics trajectory of a lipid bilayer of 1024 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 62 mol%) and 640 CHOL (cholesterol, 38 mol%) at 298.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (434176 atoms). Deposited as NMRlipids Databank simulation 550 and available from https://doi.org/10.5281/zenodo.5767451. + description: Molecular dynamics trajectory of a lipid bilayer of 1024 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 62 mol%) and 640 CHOL (cholesterol, 38 mol%) at 298.15 K. Simulated with CHARMM36 + in GROMACS for 1001 ns (434176 atoms). Deposited as NMRlipids Databank simulation + 550 and available from https://doi.org/10.5281/zenodo.5767451. sameAs: https://doi.org/10.5281/zenodo.5767451 datePublished: '2021-12-08' license: diff --git a/Simulations/137/dd2/137dd23bf6457ff74ed7684e346051d368898a35/2cc4e060bef9abe28600c2098a339638620a65d0/README.yaml b/Simulations/137/dd2/137dd23bf6457ff74ed7684e346051d368898a35/2cc4e060bef9abe28600c2098a339638620a65d0/README.yaml index 22ffd034f5..f280a8cde5 100644 --- a/Simulations/137/dd2/137dd23bf6457ff74ed7684e346051d368898a35/2cc4e060bef9abe28600c2098a339638620a65d0/README.yaml +++ b/Simulations/137/dd2/137dd23bf6457ff74ed7684e346051d368898a35/2cc4e060bef9abe28600c2098a339638620a65d0/README.yaml @@ -56,9 +56,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 169 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPS/SOD (71:14:14) bilayer at 298 K (GROMOS-CKP, Berger/Chiu NH3 charges and PME, GROMACS, 100 ns) [NMRlipids simulation 169] + name: Molecular dynamics trajectory of a POPC/POPS/SOD (71:14:14) bilayer at 298 + K (GROMOS-CKP, Berger/Chiu NH3 charges and PME, GROMACS, 100 ns) [NMRlipids simulation + 169] alternateName: 110POPC_22POPS_4620SOL_22SOD_298K_GROMOS-CKP_v1 - description: Molecular dynamics trajectory of a lipid bilayer of 110 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 71 mol%), 22 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 14 mol%) and 22 SOD (14 mol%) at 298 K. Simulated with GROMOS-CKP, Berger/Chiu NH3 charges and PME in GROMACS for 100 ns (20812 atoms). Deposited as NMRlipids Databank simulation 169 and available from https://doi.org/10.5281/zenodo.1283331. + description: Molecular dynamics trajectory of a lipid bilayer of 110 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 71 mol%), 22 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 14 mol%) + and 22 SOD (14 mol%) at 298 K. Simulated with GROMOS-CKP, Berger/Chiu NH3 charges + and PME in GROMACS for 100 ns (20812 atoms). Deposited as NMRlipids Databank simulation + 169 and available from https://doi.org/10.5281/zenodo.1283331. sameAs: https://doi.org/10.5281/zenodo.1283331 datePublished: '2018-06-05' license: @@ -147,7 +153,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1283331 identifier: 10.5281/zenodo.1283331 url: https://doi.org/10.5281/zenodo.1283331 - name: Gromos-Ckp Pops/Popc Simulations (Versions 1 And 2) 298 K With Berger/Chiu Nh3 Charges And Pme + name: Gromos-Ckp Pops/Popc Simulations (Versions 1 And 2) 298 K With Berger/Chiu + Nh3 Charges And Pme publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/138/f70/138f7086835a989159b9451f34668b197c0879ad/6eda577f480bda5448c5a5c57ad5c45097241816/README.yaml b/Simulations/138/f70/138f7086835a989159b9451f34668b197c0879ad/6eda577f480bda5448c5a5c57ad5c45097241816/README.yaml index 85572c8b90..5eb48e27af 100644 --- a/Simulations/138/f70/138f7086835a989159b9451f34668b197c0879ad/6eda577f480bda5448c5a5c57ad5c45097241816/README.yaml +++ b/Simulations/138/f70/138f7086835a989159b9451f34668b197c0879ad/6eda577f480bda5448c5a5c57ad5c45097241816/README.yaml @@ -44,9 +44,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 586 bioschema_properties: - name: Molecular dynamics trajectory of a DPPE bilayer at 342 K (GROMOS-CKP, GROMACS 5.0.6, 400 ns) [NMRlipids simulation 586] + name: Molecular dynamics trajectory of a DPPE bilayer at 342 K (GROMOS-CKP, GROMACS + 5.0.6, 400 ns) [NMRlipids simulation 586] alternateName: 128DPPE_3655SOL_342K_GROMOS-CKP_v2 - description: Molecular dynamics trajectory of a lipid bilayer of 128 DPPE (1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine) at 342 K. Simulated with GROMOS-CKP in GROMACS 5.0.6 for 400 ns (17365 atoms). Deposited as NMRlipids Databank simulation 586 and available from https://doi.org/10.5281/zenodo.1293957. + description: Molecular dynamics trajectory of a lipid bilayer of 128 DPPE (1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine) + at 342 K. Simulated with GROMOS-CKP in GROMACS 5.0.6 for 400 ns (17365 atoms). + Deposited as NMRlipids Databank simulation 586 and available from https://doi.org/10.5281/zenodo.1293957. sameAs: https://doi.org/10.5281/zenodo.1293957 datePublished: '2018-06-20' license: diff --git a/Simulations/13b/0b5/13b0b5e80da6f67f5eb81c39a9f08fdf9f33191e/763ad0b3d8170ca557f95343e16ac8e92072fa0f/README.yaml b/Simulations/13b/0b5/13b0b5e80da6f67f5eb81c39a9f08fdf9f33191e/763ad0b3d8170ca557f95343e16ac8e92072fa0f/README.yaml index b94ce7377b..c6284c4d0d 100644 --- a/Simulations/13b/0b5/13b0b5e80da6f67f5eb81c39a9f08fdf9f33191e/763ad0b3d8170ca557f95343e16ac8e92072fa0f/README.yaml +++ b/Simulations/13b/0b5/13b0b5e80da6f67f5eb81c39a9f08fdf9f33191e/763ad0b3d8170ca557f95343e16ac8e92072fa0f/README.yaml @@ -44,9 +44,13 @@ EXPERIMENT: SLiPC: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a SLiPC bilayer at 333.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 637] + name: Molecular dynamics trajectory of a SLiPC bilayer at 333.15 K (CHARMM36, GROMACS, + 1001 ns) [NMRlipids simulation 637] alternateName: 256SLiPC_12800SOL_333K - description: Molecular dynamics trajectory of a lipid bilayer of 256 SLiPC (1-(18:0)-2-(18:2 $^{\Delta9,12}$)-sn-glycero-3-phosphocholine) at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (73728 atoms). Deposited as NMRlipids Databank simulation 637 and available from https://doi.org/10.5281/zenodo.6943413. + description: Molecular dynamics trajectory of a lipid bilayer of 256 SLiPC (1-(18:0)-2-(18:2 + $^{\Delta9,12}$)-sn-glycero-3-phosphocholine) at 333.15 K. Simulated with CHARMM36 + in GROMACS for 1001 ns (73728 atoms). Deposited as NMRlipids Databank simulation + 637 and available from https://doi.org/10.5281/zenodo.6943413. sameAs: https://doi.org/10.5281/zenodo.6943413 datePublished: '2022-07-30' license: @@ -134,7 +138,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.6943413 identifier: 10.5281/zenodo.6943413 url: https://doi.org/10.5281/zenodo.6943413 - name: Simulations of different single-component bilayers, three different system sizes + name: Simulations of different single-component bilayers, three different system + sizes publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/140/4bd/1404bd22d9b4689761dd7aadb026a46bea7f73f5/a2daf8e90c414895a94c77222836debe5f1721f0/README.yaml b/Simulations/140/4bd/1404bd22d9b4689761dd7aadb026a46bea7f73f5/a2daf8e90c414895a94c77222836debe5f1721f0/README.yaml index d9a370cab6..cd3d0d325a 100644 --- a/Simulations/140/4bd/1404bd22d9b4689761dd7aadb026a46bea7f73f5/a2daf8e90c414895a94c77222836debe5f1721f0/README.yaml +++ b/Simulations/140/4bd/1404bd22d9b4689761dd7aadb026a46bea7f73f5/a2daf8e90c414895a94c77222836debe5f1721f0/README.yaml @@ -53,9 +53,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 225 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (73:18:9) bilayer at 310.15 K (CHARMM36 NBFIX Han, GROMACS, 432 ns) [NMRlipids simulation 225] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (73:18:9) bilayer at 310.15 + K (CHARMM36 NBFIX Han, GROMACS, 432 ns) [NMRlipids simulation 225] alternateName: 200POPC_9000SOL_25CAL_50CLA_310K_NBFIXHan - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 73 mol%), 50 CLA (18 mol%) and 25 CAL (9 mol%) at 310.15 K. Simulated with CHARMM36 NBFIX Han in GROMACS for 432 ns (53875 atoms). Deposited as NMRlipids Databank simulation 225 and available from https://doi.org/10.5281/zenodo.3434396. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 73 mol%), 50 CLA (18 mol%) and 25 CAL (9 mol%) at 310.15 K. Simulated with CHARMM36 + NBFIX Han in GROMACS for 432 ns (53875 atoms). Deposited as NMRlipids Databank + simulation 225 and available from https://doi.org/10.5281/zenodo.3434396. sameAs: https://doi.org/10.5281/zenodo.3434396 datePublished: '2019-09-17' license: diff --git a/Simulations/144/922/144922f3b678f74edd34e33d582d8e90079353c6/daa44903d8c7513f82d4be1999a50f1157ae679d/FormFactorQuality.json b/Simulations/144/922/144922f3b678f74edd34e33d582d8e90079353c6/daa44903d8c7513f82d4be1999a50f1157ae679d/FormFactorQuality.json new file mode 100644 index 0000000000..93e1da303c --- /dev/null +++ b/Simulations/144/922/144922f3b678f74edd34e33d582d8e90079353c6/daa44903d8c7513f82d4be1999a50f1157ae679d/FormFactorQuality.json @@ -0,0 +1 @@ +[0.4703, 93.0936] \ No newline at end of file diff --git a/Simulations/144/922/144922f3b678f74edd34e33d582d8e90079353c6/daa44903d8c7513f82d4be1999a50f1157ae679d/README.yaml b/Simulations/144/922/144922f3b678f74edd34e33d582d8e90079353c6/daa44903d8c7513f82d4be1999a50f1157ae679d/README.yaml index 153808906f..6fda50b1fb 100644 --- a/Simulations/144/922/144922f3b678f74edd34e33d582d8e90079353c6/daa44903d8c7513f82d4be1999a50f1157ae679d/README.yaml +++ b/Simulations/144/922/144922f3b678f74edd34e33d582d8e90079353c6/daa44903d8c7513f82d4be1999a50f1157ae679d/README.yaml @@ -39,3 +39,8 @@ NUMBER_OF_ATOMS: 53000 DATEOFRUNNING: 15/09/2026 TYPEOFSYSTEM: lipid bilayer ID: 932 +EXPERIMENT: + ORDERPARAMETER: + DPPC: [] + FORMFACTOR: + - 10.1016/j.bbamem.2011.07.022/4 diff --git a/Simulations/144/bd9/144bd9cb8aa89380b6c8d85e98cb57f3bb8896ec/216c50de5fb3991efea46db24c5f104fd0255ffa/README.yaml b/Simulations/144/bd9/144bd9cb8aa89380b6c8d85e98cb57f3bb8896ec/216c50de5fb3991efea46db24c5f104fd0255ffa/README.yaml index 15cc86b667..175882cce1 100644 --- a/Simulations/144/bd9/144bd9cb8aa89380b6c8d85e98cb57f3bb8896ec/216c50de5fb3991efea46db24c5f104fd0255ffa/README.yaml +++ b/Simulations/144/bd9/144bd9cb8aa89380b6c8d85e98cb57f3bb8896ec/216c50de5fb3991efea46db24c5f104fd0255ffa/README.yaml @@ -67,9 +67,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 387 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/POT/POPS/SOD (37:24:24:7:7) bilayer at 298 K (ECC-lipids, GROMACS 2018.0, 975 ns) [NMRlipids simulation 387] + name: Molecular dynamics trajectory of a POPC/CLA/POT/POPS/SOD (37:24:24:7:7) bilayer + at 298 K (ECC-lipids, GROMACS 2018.0, 975 ns) [NMRlipids simulation 387] alternateName: 12POPS_60POPC_3483SOL_12SOD_39POT_39CLA_298K - description: Molecular dynamics trajectory of a lipid bilayer of 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 37 mol%), 39 CLA (24 mol%), 39 POT (24 mol%), 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 7 mol%) and 12 SOD (7 mol%) at 298 K. Simulated with ECC-lipids in GROMACS 2018.0 for 975 ns (20103 atoms). Deposited as NMRlipids Databank simulation 387 and available from https://doi.org/10.5281/zenodo.3332778. + description: Molecular dynamics trajectory of a lipid bilayer of 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 37 mol%), 39 CLA (24 mol%), 39 POT (24 mol%), 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, + 7 mol%) and 12 SOD (7 mol%) at 298 K. Simulated with ECC-lipids in GROMACS 2018.0 + for 975 ns (20103 atoms). Deposited as NMRlipids Databank simulation 387 and available + from https://doi.org/10.5281/zenodo.3332778. sameAs: https://doi.org/10.5281/zenodo.3332778 datePublished: '2018-11-14' license: @@ -162,7 +167,9 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3332778 identifier: 10.5281/zenodo.3332778 url: https://doi.org/10.5281/zenodo.3332778 - name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS (5:1) with ECC-lipids force field, and Na+ (K+) counterions at various additional concentrations of NaCl and KCl + name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS + (5:1) with ECC-lipids force field, and Na+ (K+) counterions at various additional + concentrations of NaCl and KCl publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/149/281/149281ea65b1adb21d954490f41cca37ec81c03a/c03d345271e28fc1afa559373c301ec243543886/README.yaml b/Simulations/149/281/149281ea65b1adb21d954490f41cca37ec81c03a/c03d345271e28fc1afa559373c301ec243543886/README.yaml index 4757ef4623..76a9c7e9fe 100644 --- a/Simulations/149/281/149281ea65b1adb21d954490f41cca37ec81c03a/c03d345271e28fc1afa559373c301ec243543886/README.yaml +++ b/Simulations/149/281/149281ea65b1adb21d954490f41cca37ec81c03a/c03d345271e28fc1afa559373c301ec243543886/README.yaml @@ -50,9 +50,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 498 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (83:9:9) bilayer at 370 K (Slipids for lipids and Smith & Dang for ions, GROMACS 4.6, 200 ns) [NMRlipids simulation 498] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (83:9:9) bilayer at 370 K + (Slipids for lipids and Smith & Dang for ions, GROMACS 4.6, 200 ns) [NMRlipids + simulation 498] alternateName: 200POPC_9000SOL_21SOD_21CLA_370K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 83 mol%), 21 CLA (9 mol%) and 21 SOD (9 mol%) at 370 K. Simulated with Slipids for lipids and Smith & Dang for ions in GROMACS 4.6 for 200 ns (53842 atoms). Deposited as NMRlipids Databank simulation 498 and available from https://doi.org/10.5281/zenodo.259335. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 83 mol%), 21 CLA (9 mol%) and 21 SOD (9 mol%) at 370 K. Simulated with Slipids + for lipids and Smith & Dang for ions in GROMACS 4.6 for 200 ns (53842 atoms). + Deposited as NMRlipids Databank simulation 498 and available from https://doi.org/10.5281/zenodo.259335. sameAs: https://doi.org/10.5281/zenodo.259335 datePublished: '2017-01-24' license: @@ -140,7 +145,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.259335 identifier: 10.5281/zenodo.259335 url: https://doi.org/10.5281/zenodo.259335 - name: Popc With Varying Amounts Of Cholesterol, 130 Mm Of Nacl. Slipids With Ions By Smith & Dang + name: Popc With Varying Amounts Of Cholesterol, 130 Mm Of Nacl. Slipids With Ions + By Smith & Dang publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/14d/087/14d0877ce72d8efb3ca98991ab5bd444eff16050/a1f214040627f0ddcdb1913c0c6cc2fc86dab961/README.yaml b/Simulations/14d/087/14d0877ce72d8efb3ca98991ab5bd444eff16050/a1f214040627f0ddcdb1913c0c6cc2fc86dab961/README.yaml index d6295a6bbe..00e7335621 100644 --- a/Simulations/14d/087/14d0877ce72d8efb3ca98991ab5bd444eff16050/a1f214040627f0ddcdb1913c0c6cc2fc86dab961/README.yaml +++ b/Simulations/14d/087/14d0877ce72d8efb3ca98991ab5bd444eff16050/a1f214040627f0ddcdb1913c0c6cc2fc86dab961/README.yaml @@ -50,9 +50,13 @@ WARNINGS: PBC: z-jumps ID: 311 bioschema_properties: - name: Molecular dynamics trajectory of a POPS/POT (50:50) bilayer at 298 K (Lipid17 and Dang ions, GROMACS 2018.0, 1000 ns) [NMRlipids simulation 311] + name: Molecular dynamics trajectory of a POPS/POT (50:50) bilayer at 298 K (Lipid17 + and Dang ions, GROMACS 2018.0, 1000 ns) [NMRlipids simulation 311] alternateName: 72POPS_3600SOL_72POT_298K - description: Molecular dynamics trajectory of a lipid bilayer of 72 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 50 mol%) and 72 POT (50 mol%) at 298 K. Simulated with Lipid17 and Dang ions in GROMACS 2018.0 for 1000 ns (20016 atoms). Deposited as NMRlipids Databank simulation 311 and available from https://doi.org/10.5281/zenodo.1487761. + description: Molecular dynamics trajectory of a lipid bilayer of 72 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, + 50 mol%) and 72 POT (50 mol%) at 298 K. Simulated with Lipid17 and Dang ions in + GROMACS 2018.0 for 1000 ns (20016 atoms). Deposited as NMRlipids Databank simulation + 311 and available from https://doi.org/10.5281/zenodo.1487761. sameAs: https://doi.org/10.5281/zenodo.1487761 datePublished: '2018-11-14' license: @@ -141,7 +145,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1487761 identifier: 10.5281/zenodo.1487761 url: https://doi.org/10.5281/zenodo.1487761 - name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS with the lipid17 force field, only counterions, and CaCl2 concentrations + name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS + with the lipid17 force field, only counterions, and CaCl2 concentrations publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/154/32a/15432a86e2fe83bbb98801da6790567ae983fe58/de431264bc7ef1a732d76af339ef2bbf06bda33c/README.yaml b/Simulations/154/32a/15432a86e2fe83bbb98801da6790567ae983fe58/de431264bc7ef1a732d76af339ef2bbf06bda33c/README.yaml index 23e562e759..7615dac648 100644 --- a/Simulations/154/32a/15432a86e2fe83bbb98801da6790567ae983fe58/de431264bc7ef1a732d76af339ef2bbf06bda33c/README.yaml +++ b/Simulations/154/32a/15432a86e2fe83bbb98801da6790567ae983fe58/de431264bc7ef1a732d76af339ef2bbf06bda33c/README.yaml @@ -53,9 +53,13 @@ EXPERIMENT: - 10.1039/C4SM00066H/3 ID: 597 bioschema_properties: - name: Molecular dynamics trajectory of a POPS/SOD (50:50) bilayer at 298 K (GROMOS-CKP, Berger/Chiu NH3 charges and PME, GROMACS, 100 ns) [NMRlipids simulation 597] + name: Molecular dynamics trajectory of a POPS/SOD (50:50) bilayer at 298 K (GROMOS-CKP, + Berger/Chiu NH3 charges and PME, GROMACS, 100 ns) [NMRlipids simulation 597] alternateName: 128POPS_4480SOL_128SOD_298K_GROMOS-CKP_v2 - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 50 mol%) and 128 SOD (50 mol%) at 298 K. Simulated with GROMOS-CKP, Berger/Chiu NH3 charges and PME in GROMACS for 100 ns (20608 atoms). Deposited as NMRlipids Databank simulation 597 and available from https://doi.org/10.5281/zenodo.1129431. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, + 50 mol%) and 128 SOD (50 mol%) at 298 K. Simulated with GROMOS-CKP, Berger/Chiu + NH3 charges and PME in GROMACS for 100 ns (20608 atoms). Deposited as NMRlipids + Databank simulation 597 and available from https://doi.org/10.5281/zenodo.1129431. sameAs: https://doi.org/10.5281/zenodo.1129431 datePublished: '2017-12-24' license: @@ -148,7 +152,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1129431 identifier: 10.5281/zenodo.1129431 url: https://doi.org/10.5281/zenodo.1129431 - name: Gromos-Ckp Pops Simulations (Versions 1 And 2) 298 K With Berger/Chiu Nh3 Charges And Pme + name: Gromos-Ckp Pops Simulations (Versions 1 And 2) 298 K With Berger/Chiu Nh3 + Charges And Pme publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/155/103/1551032d0e5724f346b2643eaecb5550b449816b/cd9a5571dd97171a2dfe82c09b7e138006e42a30/README.yaml b/Simulations/155/103/1551032d0e5724f346b2643eaecb5550b449816b/cd9a5571dd97171a2dfe82c09b7e138006e42a30/README.yaml index 542cd64979..5c2d450bb2 100644 --- a/Simulations/155/103/1551032d0e5724f346b2643eaecb5550b449816b/cd9a5571dd97171a2dfe82c09b7e138006e42a30/README.yaml +++ b/Simulations/155/103/1551032d0e5724f346b2643eaecb5550b449816b/cd9a5571dd97171a2dfe82c09b7e138006e42a30/README.yaml @@ -49,9 +49,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 220 bioschema_properties: - name: Molecular dynamics trajectory of a SOD/POPG/CLA (50:46:4) bilayer at 310 K (Lipid17, GROMACS 2020.1, 100 ns) [NMRlipids simulation 220] + name: Molecular dynamics trajectory of a SOD/POPG/CLA (50:46:4) bilayer at 310 K + (Lipid17, GROMACS 2020.1, 100 ns) [NMRlipids simulation 220] alternateName: 500POPG_549SOD_49CLA_25000SOL_310K - description: Molecular dynamics trajectory of a lipid bilayer of 549 SOD (50 mol%), 500 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 46 mol%) and 49 CLA (4 mol%) at 310 K. Simulated with Lipid17 in GROMACS 2020.1 for 100 ns (139098 atoms). Deposited as NMRlipids Databank simulation 220 and available from https://doi.org/10.5281/zenodo.4386514. + description: Molecular dynamics trajectory of a lipid bilayer of 549 SOD (50 mol%), + 500 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 46 mol%) and 49 CLA + (4 mol%) at 310 K. Simulated with Lipid17 in GROMACS 2020.1 for 100 ns (139098 + atoms). Deposited as NMRlipids Databank simulation 220 and available from https://doi.org/10.5281/zenodo.4386514. sameAs: https://doi.org/10.5281/zenodo.4386514 datePublished: '2019-02-20' license: @@ -142,7 +146,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.4386514 identifier: 10.5281/zenodo.4386514 url: https://doi.org/10.5281/zenodo.4386514 - name: LIPID17 POPG Bilayer Simulation (Last 100 ns, 150 mM NaCl, 310 K ) using dihedral type 9 + name: LIPID17 POPG Bilayer Simulation (Last 100 ns, 150 mM NaCl, 310 K ) using + dihedral type 9 publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/162/740/1627408784caa93cf0df4bace7100f340889f545/9306d0e7e4de2f8a3f09381533e902c110946dfe/README.yaml b/Simulations/162/740/1627408784caa93cf0df4bace7100f340889f545/9306d0e7e4de2f8a3f09381533e902c110946dfe/README.yaml index bb60b12682..b694591874 100644 --- a/Simulations/162/740/1627408784caa93cf0df4bace7100f340889f545/9306d0e7e4de2f8a3f09381533e902c110946dfe/README.yaml +++ b/Simulations/162/740/1627408784caa93cf0df4bace7100f340889f545/9306d0e7e4de2f8a3f09381533e902c110946dfe/README.yaml @@ -50,9 +50,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 49 bioschema_properties: - name: Molecular dynamics trajectory of a SOD/POPG/CLA (50:46:4) bilayer at 310 K (Slipids, GROMACS 5.1.2, 100 ns) [NMRlipids simulation 49] + name: Molecular dynamics trajectory of a SOD/POPG/CLA (50:46:4) bilayer at 310 K + (Slipids, GROMACS 5.1.2, 100 ns) [NMRlipids simulation 49] alternateName: 500POPG_25000SOL_549SOD_39CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 549 SOD (50 mol%), 500 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 46 mol%) and 49 CLA (4 mol%) at 310 K. Simulated with Slipids in GROMACS 5.1.2 for 100 ns (139098 atoms). Deposited as NMRlipids Databank simulation 49 and available from https://doi.org/10.5281/zenodo.3269320. + description: Molecular dynamics trajectory of a lipid bilayer of 549 SOD (50 mol%), + 500 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 46 mol%) and 49 CLA + (4 mol%) at 310 K. Simulated with Slipids in GROMACS 5.1.2 for 100 ns (139098 + atoms). Deposited as NMRlipids Databank simulation 49 and available from https://doi.org/10.5281/zenodo.3269320. sameAs: https://doi.org/10.5281/zenodo.3269320 datePublished: '2019-02-20' license: diff --git a/Simulations/163/102/1631022ba6901c0bb1f68ff9ab8fa3851b8c0e70/216c0fed1c8581f5308c5e2547514d37305b1da2/README.yaml b/Simulations/163/102/1631022ba6901c0bb1f68ff9ab8fa3851b8c0e70/216c0fed1c8581f5308c5e2547514d37305b1da2/README.yaml index 23dcf133e5..4adae08d62 100644 --- a/Simulations/163/102/1631022ba6901c0bb1f68ff9ab8fa3851b8c0e70/216c0fed1c8581f5308c5e2547514d37305b1da2/README.yaml +++ b/Simulations/163/102/1631022ba6901c0bb1f68ff9ab8fa3851b8c0e70/216c0fed1c8581f5308c5e2547514d37305b1da2/README.yaml @@ -59,9 +59,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 68 bioschema_properties: - name: Molecular dynamics trajectory of a SOD/CLA/POPC/POPS (43:40:14:3) bilayer at 298 K (Lipid17 and Dang ions, GROMACS 2018.0, 1000 ns) [NMRlipids simulation 68] + name: Molecular dynamics trajectory of a SOD/CLA/POPC/POPS (43:40:14:3) bilayer + at 298 K (Lipid17 and Dang ions, GROMACS 2018.0, 1000 ns) [NMRlipids simulation + 68] alternateName: 12POPS_60POPC_3213SOL_186SOD_174CLA_298K - description: Molecular dynamics trajectory of a lipid bilayer of 186 SOD (43 mol%), 174 CLA (40 mol%), 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 14 mol%) and 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 3 mol%) at 298 K. Simulated with Lipid17 and Dang ions in GROMACS 2018.0 for 1000 ns (19563 atoms). Deposited as NMRlipids Databank simulation 68 and available from https://doi.org/10.5281/zenodo.1487895. + description: Molecular dynamics trajectory of a lipid bilayer of 186 SOD (43 mol%), + 174 CLA (40 mol%), 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 14 mol%) and 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 3 mol%) + at 298 K. Simulated with Lipid17 and Dang ions in GROMACS 2018.0 for 1000 ns (19563 + atoms). Deposited as NMRlipids Databank simulation 68 and available from https://doi.org/10.5281/zenodo.1487895. sameAs: https://doi.org/10.5281/zenodo.1487895 datePublished: '2018-11-14' license: @@ -153,7 +159,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1487895 identifier: 10.5281/zenodo.1487895 url: https://doi.org/10.5281/zenodo.1487895 - name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS with the lipid17 force field, NaCl and KCl salt concentrations + name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS + with the lipid17 force field, NaCl and KCl salt concentrations publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/164/f70/164f7048924b637b0c5113ec33c40dd9a35a6751/5c107419457aea836f8a9f6565f791e9801b2660/README.yaml b/Simulations/164/f70/164f7048924b637b0c5113ec33c40dd9a35a6751/5c107419457aea836f8a9f6565f791e9801b2660/README.yaml index 628121ac74..c64ff23646 100644 --- a/Simulations/164/f70/164f7048924b637b0c5113ec33c40dd9a35a6751/5c107419457aea836f8a9f6565f791e9801b2660/README.yaml +++ b/Simulations/164/f70/164f7048924b637b0c5113ec33c40dd9a35a6751/5c107419457aea836f8a9f6565f791e9801b2660/README.yaml @@ -57,9 +57,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 500 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL/CLA/SOD (61:26:6:6) bilayer at 310 K (Slipids for lipids and Smith & Dang for ions, GROMACS 4.6, 200 ns) [NMRlipids simulation 500] + name: Molecular dynamics trajectory of a POPC/CHOL/CLA/SOD (61:26:6:6) bilayer at + 310 K (Slipids for lipids and Smith & Dang for ions, GROMACS 4.6, 200 ns) [NMRlipids + simulation 500] alternateName: 86CHOL_200POPC_9000SOL_21SOD_21CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 61 mol%), 86 CHOL (cholesterol, 26 mol%), 21 CLA (6 mol%) and 21 SOD (6 mol%) at 310 K. Simulated with Slipids for lipids and Smith & Dang for ions in GROMACS 4.6 for 200 ns (60206 atoms). Deposited as NMRlipids Databank simulation 500 and available from https://doi.org/10.5281/zenodo.259335. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 61 mol%), 86 CHOL (cholesterol, 26 mol%), 21 CLA (6 mol%) and 21 SOD (6 mol%) + at 310 K. Simulated with Slipids for lipids and Smith & Dang for ions in GROMACS + 4.6 for 200 ns (60206 atoms). Deposited as NMRlipids Databank simulation 500 and + available from https://doi.org/10.5281/zenodo.259335. sameAs: https://doi.org/10.5281/zenodo.259335 datePublished: '2017-01-24' license: @@ -149,7 +155,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.259335 identifier: 10.5281/zenodo.259335 url: https://doi.org/10.5281/zenodo.259335 - name: Popc With Varying Amounts Of Cholesterol, 130 Mm Of Nacl. Slipids With Ions By Smith & Dang + name: Popc With Varying Amounts Of Cholesterol, 130 Mm Of Nacl. Slipids With Ions + By Smith & Dang publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/16a/1b0/16a1b09d60c0743b2a494934f04e39f4e8824686/69889af89cbaf3f9d4e75c3e8206de280e628370/README.yaml b/Simulations/16a/1b0/16a1b09d60c0743b2a494934f04e39f4e8824686/69889af89cbaf3f9d4e75c3e8206de280e628370/README.yaml index f28d1a6044..00baff51af 100644 --- a/Simulations/16a/1b0/16a1b09d60c0743b2a494934f04e39f4e8824686/69889af89cbaf3f9d4e75c3e8206de280e628370/README.yaml +++ b/Simulations/16a/1b0/16a1b09d60c0743b2a494934f04e39f4e8824686/69889af89cbaf3f9d4e75c3e8206de280e628370/README.yaml @@ -60,9 +60,14 @@ EXPERIMENT: SAPI25: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POT/CLA/SAPI25 (56:31:7:6) bilayer at 298.15 K (CHARMM36m, GROMACS 2020.1, 1200 ns) [NMRlipids simulation 784] + name: Molecular dynamics trajectory of a POPC/POT/CLA/SAPI25 (56:31:7:6) bilayer + at 298.15 K (CHARMM36m, GROMACS 2020.1, 1200 ns) [NMRlipids simulation 784] alternateName: POPC_270_SAPI25_30_KCl_150mM_298.15K - description: Molecular dynamics trajectory of a lipid bilayer of 270 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 56 mol%), 153 POT (31 mol%), 33 CLA (7 mol%) and 30 SAPI25 (1-stearoyl-2-arachidonoyl-sn-phosphatidylinositol 4,5-biphosphate, 6 mol%) at 298.15 K. Simulated with CHARMM36m in GROMACS 2020.1 for 1200 ns (79698 atoms). Deposited as NMRlipids Databank simulation 784 and available from https://doi.org/10.5281/zenodo.8370426. + description: Molecular dynamics trajectory of a lipid bilayer of 270 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 56 mol%), 153 POT (31 mol%), 33 CLA (7 mol%) and 30 SAPI25 (1-stearoyl-2-arachidonoyl-sn-phosphatidylinositol + 4,5-biphosphate, 6 mol%) at 298.15 K. Simulated with CHARMM36m in GROMACS 2020.1 + for 1200 ns (79698 atoms). Deposited as NMRlipids Databank simulation 784 and + available from https://doi.org/10.5281/zenodo.8370426. sameAs: https://doi.org/10.5281/zenodo.8370426 datePublished: '2023-09-22' license: diff --git a/Simulations/16a/a70/16aa70c118dbfdbb7bd8e0462575e2776e0dec9a/ba8633f6385dbf4c344b8a7580603620b0d52603/README.yaml b/Simulations/16a/a70/16aa70c118dbfdbb7bd8e0462575e2776e0dec9a/ba8633f6385dbf4c344b8a7580603620b0d52603/README.yaml index 647d30eb8b..a34971aa64 100644 --- a/Simulations/16a/a70/16aa70c118dbfdbb7bd8e0462575e2776e0dec9a/ba8633f6385dbf4c344b8a7580603620b0d52603/README.yaml +++ b/Simulations/16a/a70/16aa70c118dbfdbb7bd8e0462575e2776e0dec9a/ba8633f6385dbf4c344b8a7580603620b0d52603/README.yaml @@ -51,9 +51,13 @@ TRJLENGTH: 200020.0 DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 9 bioschema_properties: - name: Molecular dynamics trajectory of a CHOL/POPC (50:50) bilayer at 303 K (CHARMM36, GROMACS, 200 ns) [NMRlipids simulation 9] + name: Molecular dynamics trajectory of a CHOL/POPC (50:50) bilayer at 303 K (CHARMM36, + GROMACS, 200 ns) [NMRlipids simulation 9] alternateName: POPC50%chol_T303K - description: Molecular dynamics trajectory of a lipid bilayer of 80 CHOL (cholesterol, 50 mol%) and 80 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 50 mol%) at 303 K. Simulated with CHARMM36 in GROMACS for 200 ns (30128 atoms). Deposited as NMRlipids Databank simulation 9 and available from https://doi.org/10.5281/zenodo.14068. + description: Molecular dynamics trajectory of a lipid bilayer of 80 CHOL (cholesterol, + 50 mol%) and 80 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 50 mol%) + at 303 K. Simulated with CHARMM36 in GROMACS for 200 ns (30128 atoms). Deposited + as NMRlipids Databank simulation 9 and available from https://doi.org/10.5281/zenodo.14068. sameAs: https://doi.org/10.5281/zenodo.14068 datePublished: '2015-01-19' license: diff --git a/Simulations/16c/24c/16c24c4c4afed59906a86d25720a8ca356278d2b/9def6374b2138ea6bf9165f9366ceea12cc98569/README.yaml b/Simulations/16c/24c/16c24c4c4afed59906a86d25720a8ca356278d2b/9def6374b2138ea6bf9165f9366ceea12cc98569/README.yaml index c045fdc8fb..d7a9e5979b 100644 --- a/Simulations/16c/24c/16c24c4c4afed59906a86d25720a8ca356278d2b/9def6374b2138ea6bf9165f9366ceea12cc98569/README.yaml +++ b/Simulations/16c/24c/16c24c4c4afed59906a86d25720a8ca356278d2b/9def6374b2138ea6bf9165f9366ceea12cc98569/README.yaml @@ -53,9 +53,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/9 ID: 703 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (53:47) bilayer at 298.15 K (Slipids, GROMACS 2021, 1001 ns) [NMRlipids simulation 703] + name: Molecular dynamics trajectory of a POPC/CHOL (53:47) bilayer at 298.15 K (Slipids, + GROMACS 2021, 1001 ns) [NMRlipids simulation 703] alternateName: Slipids_POPC_CHOL47_S - description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 53 mol%) and 56 CHOL (cholesterol, 47 mol%) at 298.15 K. Simulated with Slipids in GROMACS 2021 for 1001 ns (30720 atoms). Deposited as NMRlipids Databank simulation 703 and available from https://doi.org/10.5281/zenodo.7022749. + description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 53 mol%) and 56 CHOL (cholesterol, 47 mol%) at 298.15 K. Simulated with Slipids + in GROMACS 2021 for 1001 ns (30720 atoms). Deposited as NMRlipids Databank simulation + 703 and available from https://doi.org/10.5281/zenodo.7022749. sameAs: https://doi.org/10.5281/zenodo.7022749 datePublished: '2022-08-23' license: diff --git a/Simulations/16e/05e/16e05ef76ec9e852afadd7e2bc1639becf9c153b/abdfd2e517f2b5aefdefea5ad0831e3f7d0f4ab8/README.yaml b/Simulations/16e/05e/16e05ef76ec9e852afadd7e2bc1639becf9c153b/abdfd2e517f2b5aefdefea5ad0831e3f7d0f4ab8/README.yaml index 3da55ef8cd..29792aff47 100644 --- a/Simulations/16e/05e/16e05ef76ec9e852afadd7e2bc1639becf9c153b/abdfd2e517f2b5aefdefea5ad0831e3f7d0f4ab8/README.yaml +++ b/Simulations/16e/05e/16e05ef76ec9e852afadd7e2bc1639becf9c153b/abdfd2e517f2b5aefdefea5ad0831e3f7d0f4ab8/README.yaml @@ -56,9 +56,14 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 402 bioschema_properties: - name: Molecular dynamics trajectory of a CLA/CAL/POPC/POPG (40:28:16:16) bilayer at 298 K (CHARMM36, GROMACS, 200 ns) [NMRlipids simulation 402] + name: Molecular dynamics trajectory of a CLA/CAL/POPC/POPG (40:28:16:16) bilayer + at 298 K (CHARMM36, GROMACS, 200 ns) [NMRlipids simulation 402] alternateName: 250POPC_250POPG_445CAL_640CLA_298K_1206774Atoms - description: Molecular dynamics trajectory of a lipid bilayer of 640 CLA (40 mol%), 445 CAL (28 mol%), 250 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 16 mol%) and 250 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 16 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for 200 ns (120677 atoms). Deposited as NMRlipids Databank simulation 402 and available from https://doi.org/10.5281/zenodo.3483793. + description: Molecular dynamics trajectory of a lipid bilayer of 640 CLA (40 mol%), + 445 CAL (28 mol%), 250 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 16 mol%) and 250 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 16 mol%) + at 298 K. Simulated with CHARMM36 in GROMACS for 200 ns (120677 atoms). Deposited + as NMRlipids Databank simulation 402 and available from https://doi.org/10.5281/zenodo.3483793. sameAs: https://doi.org/10.5281/zenodo.3483793 datePublished: '2019-10-12' license: diff --git a/Simulations/16e/2b1/16e2b1ba8c73d253a998d70935adad61ce3d5b61/6df200240ee666fdd0455da6c7b51d6851de5059/README.yaml b/Simulations/16e/2b1/16e2b1ba8c73d253a998d70935adad61ce3d5b61/6df200240ee666fdd0455da6c7b51d6851de5059/README.yaml index e53a5b7e0e..844bc4e59e 100644 --- a/Simulations/16e/2b1/16e2b1ba8c73d253a998d70935adad61ce3d5b61/6df200240ee666fdd0455da6c7b51d6851de5059/README.yaml +++ b/Simulations/16e/2b1/16e2b1ba8c73d253a998d70935adad61ce3d5b61/6df200240ee666fdd0455da6c7b51d6851de5059/README.yaml @@ -67,9 +67,16 @@ EXPERIMENT: SAPI25: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a CHOL/POPC/POT/CLA/SAPI25 (36:32:22:7:4) bilayer at 298.15 K (CHARMM36m, GROMACS 2020.1, 1245 ns) [NMRlipids simulation 780] + name: Molecular dynamics trajectory of a CHOL/POPC/POT/CLA/SAPI25 (36:32:22:7:4) + bilayer at 298.15 K (CHARMM36m, GROMACS 2020.1, 1245 ns) [NMRlipids simulation + 780] alternateName: POPC_134_SAPI25_16_CHOL_150_KCl_150mM_298.15K - description: Molecular dynamics trajectory of a lipid bilayer of 150 CHOL (cholesterol, 36 mol%), 134 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 32 mol%), 92 POT (22 mol%), 28 CLA (7 mol%) and 16 SAPI25 (1-stearoyl-2-arachidonoyl-sn-phosphatidylinositol 4,5-biphosphate, 4 mol%) at 298.15 K. Simulated with CHARMM36m in GROMACS 2020.1 for 1245 ns (63685 atoms). Deposited as NMRlipids Databank simulation 780 and available from https://doi.org/10.5281/zenodo.8370445. + description: Molecular dynamics trajectory of a lipid bilayer of 150 CHOL (cholesterol, + 36 mol%), 134 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 32 mol%), + 92 POT (22 mol%), 28 CLA (7 mol%) and 16 SAPI25 (1-stearoyl-2-arachidonoyl-sn-phosphatidylinositol + 4,5-biphosphate, 4 mol%) at 298.15 K. Simulated with CHARMM36m in GROMACS 2020.1 + for 1245 ns (63685 atoms). Deposited as NMRlipids Databank simulation 780 and + available from https://doi.org/10.5281/zenodo.8370445. sameAs: https://doi.org/10.5281/zenodo.8370445 datePublished: '2023-09-22' license: diff --git a/Simulations/170/92a/17092a63b14085b6445c83d0f0e69520d3ed3268/15d69a06033fcbe25db6a439fcd7206459b68c7b/README.yaml b/Simulations/170/92a/17092a63b14085b6445c83d0f0e69520d3ed3268/15d69a06033fcbe25db6a439fcd7206459b68c7b/README.yaml index 1740398939..f2932d6bcf 100644 --- a/Simulations/170/92a/17092a63b14085b6445c83d0f0e69520d3ed3268/15d69a06033fcbe25db6a439fcd7206459b68c7b/README.yaml +++ b/Simulations/170/92a/17092a63b14085b6445c83d0f0e69520d3ed3268/15d69a06033fcbe25db6a439fcd7206459b68c7b/README.yaml @@ -43,9 +43,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 811 bioschema_properties: - name: Molecular dynamics trajectory of a DMPC bilayer at 314 K (OPLS4, GROMACS Desmond 2022-2, 450 ns) [NMRlipids simulation 811] + name: Molecular dynamics trajectory of a DMPC bilayer at 314 K (OPLS4, GROMACS Desmond + 2022-2, 450 ns) [NMRlipids simulation 811] alternateName: 200DMPC_1000SOL_300K - description: Molecular dynamics trajectory of a lipid bilayer of 200 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) at 314 K. Simulated with OPLS4 in GROMACS Desmond 2022-2 for 450 ns (26600 atoms). Deposited as NMRlipids Databank simulation 811 and available from https://doi.org/10.5281/zenodo.11045998. + description: Molecular dynamics trajectory of a lipid bilayer of 200 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) + at 314 K. Simulated with OPLS4 in GROMACS Desmond 2022-2 for 450 ns (26600 atoms). + Deposited as NMRlipids Databank simulation 811 and available from https://doi.org/10.5281/zenodo.11045998. sameAs: https://doi.org/10.5281/zenodo.11045998 datePublished: '2024-04-23' license: diff --git a/Simulations/174/c74/174c746e212577c63e6df6c6910b2e9a1d587241/6fb923ea75663dbeea13c0fa79015ae11dea9157/README.yaml b/Simulations/174/c74/174c746e212577c63e6df6c6910b2e9a1d587241/6fb923ea75663dbeea13c0fa79015ae11dea9157/README.yaml index c31bb89352..09a79c78ad 100644 --- a/Simulations/174/c74/174c746e212577c63e6df6c6910b2e9a1d587241/6fb923ea75663dbeea13c0fa79015ae11dea9157/README.yaml +++ b/Simulations/174/c74/174c746e212577c63e6df6c6910b2e9a1d587241/6fb923ea75663dbeea13c0fa79015ae11dea9157/README.yaml @@ -44,9 +44,12 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 87 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC bilayer at 325 K (CHARMM36, GROMACS 5.0.4, 400 ns) [NMRlipids simulation 87] + name: Molecular dynamics trajectory of a DPPC bilayer at 325 K (CHARMM36, GROMACS + 5.0.4, 400 ns) [NMRlipids simulation 87] alternateName: 512DPPC_20480SOL_325K - description: Molecular dynamics trajectory of a lipid bilayer of 512 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) at 325 K. Simulated with CHARMM36 in GROMACS 5.0.4 for 400 ns (128000 atoms). Deposited as NMRlipids Databank simulation 87 and available from https://doi.org/10.5281/zenodo.16254. + description: Molecular dynamics trajectory of a lipid bilayer of 512 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) + at 325 K. Simulated with CHARMM36 in GROMACS 5.0.4 for 400 ns (128000 atoms). + Deposited as NMRlipids Databank simulation 87 and available from https://doi.org/10.5281/zenodo.16254. sameAs: https://doi.org/10.5281/zenodo.16254 datePublished: '2015-03-21' license: diff --git a/Simulations/17b/a53/17ba5361387ddec8a9f668c944263356aa3e20e6/c9b3ab8d53b184c8373b41a7b1882fbdf1955f58/README.yaml b/Simulations/17b/a53/17ba5361387ddec8a9f668c944263356aa3e20e6/c9b3ab8d53b184c8373b41a7b1882fbdf1955f58/README.yaml index dc64a486b8..1b1598b5d7 100644 --- a/Simulations/17b/a53/17ba5361387ddec8a9f668c944263356aa3e20e6/c9b3ab8d53b184c8373b41a7b1882fbdf1955f58/README.yaml +++ b/Simulations/17b/a53/17ba5361387ddec8a9f668c944263356aa3e20e6/c9b3ab8d53b184c8373b41a7b1882fbdf1955f58/README.yaml @@ -48,9 +48,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 513 bioschema_properties: - name: Molecular dynamics trajectory of a DOPS/SOD (50:50) bilayer at 303 K (GROMOS-CKP, GROMOS NH3 charges and PME, GROMACS, 100 ns) [NMRlipids simulation 513] + name: Molecular dynamics trajectory of a DOPS/SOD (50:50) bilayer at 303 K (GROMOS-CKP, + GROMOS NH3 charges and PME, GROMACS, 100 ns) [NMRlipids simulation 513] alternateName: 128DOPS_4480SOL_128SOD_303K_GROMOS-CKP_v1 - description: Molecular dynamics trajectory of a lipid bilayer of 128 DOPS (1,2-dioleoyl-sn-glycero-3-phospho-L-serine, 50 mol%) and 128 SOD (50 mol%) at 303 K. Simulated with GROMOS-CKP, GROMOS NH3 charges and PME in GROMACS for 100 ns (20864 atoms). Deposited as NMRlipids Databank simulation 513 and available from https://doi.org/10.5281/zenodo.1129447. + description: Molecular dynamics trajectory of a lipid bilayer of 128 DOPS (1,2-dioleoyl-sn-glycero-3-phospho-L-serine, + 50 mol%) and 128 SOD (50 mol%) at 303 K. Simulated with GROMOS-CKP, GROMOS NH3 + charges and PME in GROMACS for 100 ns (20864 atoms). Deposited as NMRlipids Databank + simulation 513 and available from https://doi.org/10.5281/zenodo.1129447. sameAs: https://doi.org/10.5281/zenodo.1129447 datePublished: '2017-12-24' license: @@ -139,7 +143,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1129447 identifier: 10.5281/zenodo.1129447 url: https://doi.org/10.5281/zenodo.1129447 - name: Gromos-Ckp Dops Simulations (Versions 1 And 2) 303 K With Gromos Nh3 Charges And Pme + name: Gromos-Ckp Dops Simulations (Versions 1 And 2) 303 K With Gromos Nh3 Charges + And Pme publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/184/43f/18443f90b28f87979d175f3da976d22153bfa22d/2e1eb3e3eca27e99b3de593698a31676c467e38d/README.yaml b/Simulations/184/43f/18443f90b28f87979d175f3da976d22153bfa22d/2e1eb3e3eca27e99b3de593698a31676c467e38d/README.yaml index 4a36167faa..f2b5c7b06b 100644 --- a/Simulations/184/43f/18443f90b28f87979d175f3da976d22153bfa22d/2e1eb3e3eca27e99b3de593698a31676c467e38d/README.yaml +++ b/Simulations/184/43f/18443f90b28f87979d175f3da976d22153bfa22d/2e1eb3e3eca27e99b3de593698a31676c467e38d/README.yaml @@ -52,9 +52,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/3 ID: 109 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (89:11) bilayer at 298.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 109] + name: Molecular dynamics trajectory of a POPC/CHOL (89:11) bilayer at 298.15 K (CHARMM36, + GROMACS, 1001 ns) [NMRlipids simulation 109] alternateName: 64POPC_8CHOL_3600SOL_298K - description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 89 mol%) and 8 CHOL (cholesterol, 11 mol%) at 298.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (19968 atoms). Deposited as NMRlipids Databank simulation 109 and available from https://doi.org/10.5281/zenodo.5767451. + description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 89 mol%) and 8 CHOL (cholesterol, 11 mol%) at 298.15 K. Simulated with CHARMM36 + in GROMACS for 1001 ns (19968 atoms). Deposited as NMRlipids Databank simulation + 109 and available from https://doi.org/10.5281/zenodo.5767451. sameAs: https://doi.org/10.5281/zenodo.5767451 datePublished: '2021-12-08' license: diff --git a/Simulations/18c/55d/18c55dbc1844f880a0b8738ac30b0837a39cc03e/18c55dbc1844f880a0b8738ac30b0837a39cc03e/README.yaml b/Simulations/18c/55d/18c55dbc1844f880a0b8738ac30b0837a39cc03e/18c55dbc1844f880a0b8738ac30b0837a39cc03e/README.yaml index a64a6a2713..0ce6afeec4 100644 --- a/Simulations/18c/55d/18c55dbc1844f880a0b8738ac30b0837a39cc03e/18c55dbc1844f880a0b8738ac30b0837a39cc03e/README.yaml +++ b/Simulations/18c/55d/18c55dbc1844f880a0b8738ac30b0837a39cc03e/18c55dbc1844f880a0b8738ac30b0837a39cc03e/README.yaml @@ -50,9 +50,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 257 bioschema_properties: - name: Molecular dynamics trajectory of a CLA/POPC/CAL (49:27:24) bilayer at 303 K (Charmm-Drude polarizable; system has been equilibriated using Charmm36, OPENMM, 4 ns) [NMRlipids simulation 257] + name: Molecular dynamics trajectory of a CLA/POPC/CAL (49:27:24) bilayer at 303 + K (Charmm-Drude polarizable; system has been equilibriated using Charmm36, OPENMM, + 4 ns) [NMRlipids simulation 257] alternateName: 128POPC_6400SOL_114CaCl2_303K - description: Molecular dynamics trajectory of a lipid bilayer of 228 CLA (49 mol%), 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 27 mol%) and 114 CAL (24 mol%) at 303 K. Simulated with Charmm-Drude polarizable; system has been equilibriated using Charmm36 in OPENMM for 4 ns (57516 atoms). Deposited as NMRlipids Databank simulation 257 and available from https://doi.org/10.5281/zenodo.5507316. + description: Molecular dynamics trajectory of a lipid bilayer of 228 CLA (49 mol%), + 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 27 mol%) and 114 CAL + (24 mol%) at 303 K. Simulated with Charmm-Drude polarizable; system has been equilibriated + using Charmm36 in OPENMM for 4 ns (57516 atoms). Deposited as NMRlipids Databank + simulation 257 and available from https://doi.org/10.5281/zenodo.5507316. sameAs: https://doi.org/10.5281/zenodo.5507316 datePublished: '2021-05-05' license: @@ -145,7 +151,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.5507316 identifier: 10.5281/zenodo.5507316 url: https://doi.org/10.5281/zenodo.5507316 - name: Pure POPC membrane simulations with 1000 mM CaCl2 with the CHARMM-Drude force field (OpenMM) + name: Pure POPC membrane simulations with 1000 mM CaCl2 with the CHARMM-Drude + force field (OpenMM) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/18c/f18/18cf180d20c946d479a1f12645e9176981cc1a05/5c831483d57c45f9a86e7894f968ca30c051f12d/README.yaml b/Simulations/18c/f18/18cf180d20c946d479a1f12645e9176981cc1a05/5c831483d57c45f9a86e7894f968ca30c051f12d/README.yaml index 9a5a1a3d8d..3514806861 100644 --- a/Simulations/18c/f18/18cf180d20c946d479a1f12645e9176981cc1a05/5c831483d57c45f9a86e7894f968ca30c051f12d/README.yaml +++ b/Simulations/18c/f18/18cf180d20c946d479a1f12645e9176981cc1a05/5c831483d57c45f9a86e7894f968ca30c051f12d/README.yaml @@ -48,9 +48,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 258 bioschema_properties: - name: Molecular dynamics trajectory of a DOPS/SOD (50:50) bilayer at 303 K (GROMOS-CKP, GROMOS NH3 charges and PME, GROMACS, 100 ns) [NMRlipids simulation 258] + name: Molecular dynamics trajectory of a DOPS/SOD (50:50) bilayer at 303 K (GROMOS-CKP, + GROMOS NH3 charges and PME, GROMACS, 100 ns) [NMRlipids simulation 258] alternateName: 128DOPS_4480SOL_128SOD_303K_GROMOS-CKP_v2 - description: Molecular dynamics trajectory of a lipid bilayer of 128 DOPS (1,2-dioleoyl-sn-glycero-3-phospho-L-serine, 50 mol%) and 128 SOD (50 mol%) at 303 K. Simulated with GROMOS-CKP, GROMOS NH3 charges and PME in GROMACS for 100 ns (20864 atoms). Deposited as NMRlipids Databank simulation 258 and available from https://doi.org/10.5281/zenodo.1129447. + description: Molecular dynamics trajectory of a lipid bilayer of 128 DOPS (1,2-dioleoyl-sn-glycero-3-phospho-L-serine, + 50 mol%) and 128 SOD (50 mol%) at 303 K. Simulated with GROMOS-CKP, GROMOS NH3 + charges and PME in GROMACS for 100 ns (20864 atoms). Deposited as NMRlipids Databank + simulation 258 and available from https://doi.org/10.5281/zenodo.1129447. sameAs: https://doi.org/10.5281/zenodo.1129447 datePublished: '2017-12-24' license: @@ -139,7 +143,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1129447 identifier: 10.5281/zenodo.1129447 url: https://doi.org/10.5281/zenodo.1129447 - name: Gromos-Ckp Dops Simulations (Versions 1 And 2) 303 K With Gromos Nh3 Charges And Pme + name: Gromos-Ckp Dops Simulations (Versions 1 And 2) 303 K With Gromos Nh3 Charges + And Pme publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/18e/794/18e7944e27be44e0efbb90590c5f88ca29664652/350258dcc317cd9f2bf313b978af19781b5f74cd/README.yaml b/Simulations/18e/794/18e7944e27be44e0efbb90590c5f88ca29664652/350258dcc317cd9f2bf313b978af19781b5f74cd/README.yaml index 4f9e04e9b8..1abd7d1a9b 100644 --- a/Simulations/18e/794/18e7944e27be44e0efbb90590c5f88ca29664652/350258dcc317cd9f2bf313b978af19781b5f74cd/README.yaml +++ b/Simulations/18e/794/18e7944e27be44e0efbb90590c5f88ca29664652/350258dcc317cd9f2bf313b978af19781b5f74cd/README.yaml @@ -52,9 +52,14 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 125 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPS/POT (33:33:33) bilayer at 298 K (CHARMM36, GROMACS, 200 ns) [NMRlipids simulation 125] + name: Molecular dynamics trajectory of a POPC/POPS/POT (33:33:33) bilayer at 298 + K (CHARMM36, GROMACS, 200 ns) [NMRlipids simulation 125] alternateName: 150POPC_150POPS_150POT_298K_71655Atoms - description: Molecular dynamics trajectory of a lipid bilayer of 150 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 33 mol%), 150 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 33 mol%) and 150 POT (33 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for 200 ns (71655 atoms). Deposited as NMRlipids Databank simulation 125 and available from https://doi.org/10.5281/zenodo.2542164. + description: Molecular dynamics trajectory of a lipid bilayer of 150 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 33 mol%), 150 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 33 mol%) + and 150 POT (33 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for 200 ns + (71655 atoms). Deposited as NMRlipids Databank simulation 125 and available from + https://doi.org/10.5281/zenodo.2542164. sameAs: https://doi.org/10.5281/zenodo.2542164 datePublished: '2019-01-16' license: diff --git a/Simulations/190/463/1904639f46788801d29a5f44f015048174bcf6b4/97cde4b14332cf79b9cd757e8d08a132f0e73223/README.yaml b/Simulations/190/463/1904639f46788801d29a5f44f015048174bcf6b4/97cde4b14332cf79b9cd757e8d08a132f0e73223/README.yaml index 78be52b34d..b4e70e4ac0 100644 --- a/Simulations/190/463/1904639f46788801d29a5f44f015048174bcf6b4/97cde4b14332cf79b9cd757e8d08a132f0e73223/README.yaml +++ b/Simulations/190/463/1904639f46788801d29a5f44f015048174bcf6b4/97cde4b14332cf79b9cd757e8d08a132f0e73223/README.yaml @@ -40,9 +40,12 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 255 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC bilayer at 358 K (CHARMM36, GROMACS 2020, 25 ns) [NMRlipids simulation 255] + name: Molecular dynamics trajectory of a DPPC bilayer at 358 K (CHARMM36, GROMACS + 2020, 25 ns) [NMRlipids simulation 255] alternateName: 256DPPC_42642SOL_358K - description: Molecular dynamics trajectory of a lipid bilayer of 256 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) at 358 K. Simulated with CHARMM36 in GROMACS 2020 for 25 ns (161206 atoms). Deposited as NMRlipids Databank simulation 255 and available from https://doi.org/10.5281/zenodo.4300706. + description: Molecular dynamics trajectory of a lipid bilayer of 256 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) + at 358 K. Simulated with CHARMM36 in GROMACS 2020 for 25 ns (161206 atoms). Deposited + as NMRlipids Databank simulation 255 and available from https://doi.org/10.5281/zenodo.4300706. sameAs: https://doi.org/10.5281/zenodo.4300706 datePublished: '2020-12-01' license: @@ -135,7 +138,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.4300706 identifier: 10.5281/zenodo.4300706 url: https://doi.org/10.5281/zenodo.4300706 - name: 256 DPPC Molecules bilayer in pure Water, simulated at 288K (gel) or 358K (fluid) + name: 256 DPPC Molecules bilayer in pure Water, simulated at 288K (gel) or 358K + (fluid) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/191/aaf/191aaff24d55b8b30c54ad09a83e6e8123e0e501/37691cff044a4aeffa17efa855a65c987ad5bbdf/README.yaml b/Simulations/191/aaf/191aaff24d55b8b30c54ad09a83e6e8123e0e501/37691cff044a4aeffa17efa855a65c987ad5bbdf/README.yaml index 515d7f0f88..7f7c598a3a 100644 --- a/Simulations/191/aaf/191aaff24d55b8b30c54ad09a83e6e8123e0e501/37691cff044a4aeffa17efa855a65c987ad5bbdf/README.yaml +++ b/Simulations/191/aaf/191aaff24d55b8b30c54ad09a83e6e8123e0e501/37691cff044a4aeffa17efa855a65c987ad5bbdf/README.yaml @@ -67,9 +67,15 @@ EXPERIMENT: SAPI25: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POT/CHOL/CLA/SAPI25 (56:22:11:7:4) bilayer at 298.15 K (CHARMM36m, GROMACS 2020.1, 1206 ns) [NMRlipids simulation 783] + name: Molecular dynamics trajectory of a POPC/POT/CHOL/CLA/SAPI25 (56:22:11:7:4) + bilayer at 298.15 K (CHARMM36m, GROMACS 2020.1, 1206 ns) [NMRlipids simulation + 783] alternateName: POPC_238_SAPI25_16_CHOL_46_KCl_150mM_298.15K - description: Molecular dynamics trajectory of a lipid bilayer of 238 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 56 mol%), 96 POT (22 mol%), 46 CHOL (cholesterol, 11 mol%), 32 CLA (7 mol%) and 16 SAPI25 (1-stearoyl-2-arachidonoyl-sn-phosphatidylinositol 4,5-biphosphate, 4 mol%) at 298.15 K. Simulated with CHARMM36m in GROMACS 2020.1 for 1206 ns (75159 atoms). Deposited as NMRlipids Databank simulation 783 and available from https://doi.org/10.5281/zenodo.8370440. + description: Molecular dynamics trajectory of a lipid bilayer of 238 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 56 mol%), 96 POT (22 mol%), 46 CHOL (cholesterol, 11 mol%), 32 CLA (7 mol%) and + 16 SAPI25 (1-stearoyl-2-arachidonoyl-sn-phosphatidylinositol 4,5-biphosphate, + 4 mol%) at 298.15 K. Simulated with CHARMM36m in GROMACS 2020.1 for 1206 ns (75159 + atoms). Deposited as NMRlipids Databank simulation 783 and available from https://doi.org/10.5281/zenodo.8370440. sameAs: https://doi.org/10.5281/zenodo.8370440 datePublished: '2023-09-22' license: diff --git a/Simulations/19e/f1b/19ef1b2957f3fd59f5633581a55f8afd61788f08/4203213cd437b309b98debf97e0df15a71c19ce2/README.yaml b/Simulations/19e/f1b/19ef1b2957f3fd59f5633581a55f8afd61788f08/4203213cd437b309b98debf97e0df15a71c19ce2/README.yaml index 2cd3a04b72..e9418df140 100644 --- a/Simulations/19e/f1b/19ef1b2957f3fd59f5633581a55f8afd61788f08/4203213cd437b309b98debf97e0df15a71c19ce2/README.yaml +++ b/Simulations/19e/f1b/19ef1b2957f3fd59f5633581a55f8afd61788f08/4203213cd437b309b98debf97e0df15a71c19ce2/README.yaml @@ -49,9 +49,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 570 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/CHOL (80:20) bilayer at 310 K (CHARMM36, GROMACS, 1000 ns) [NMRlipids simulation 570] + name: Molecular dynamics trajectory of a DPPC/CHOL (80:20) bilayer at 310 K (CHARMM36, + GROMACS, 1000 ns) [NMRlipids simulation 570] alternateName: 128DPPC_4800SOL_32CHOL_310K - description: Molecular dynamics trajectory of a lipid bilayer of 128 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 80 mol%) and 32 CHOL (cholesterol, 20 mol%) at 310 K. Simulated with CHARMM36 in GROMACS for 1000 ns (33408 atoms). Deposited as NMRlipids Databank simulation 570 and available from https://doi.org/10.5281/zenodo.1010131. + description: Molecular dynamics trajectory of a lipid bilayer of 128 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 80 mol%) and 32 CHOL (cholesterol, 20 mol%) at 310 K. Simulated with CHARMM36 + in GROMACS for 1000 ns (33408 atoms). Deposited as NMRlipids Databank simulation + 570 and available from https://doi.org/10.5281/zenodo.1010131. sameAs: https://doi.org/10.5281/zenodo.1010131 datePublished: '2017-10-13' license: @@ -146,7 +150,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1010131 identifier: 10.5281/zenodo.1010131 url: https://doi.org/10.5281/zenodo.1010131 - name: Set Simulations Small Pure Bilayers With Cholesterol (Max 128 Lipids) Using Charmm36 Ff In Gromacs (Dppc) + name: Set Simulations Small Pure Bilayers With Cholesterol (Max 128 Lipids) Using + Charmm36 Ff In Gromacs (Dppc) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/1a0/277/1a02776e006c5309008deeb88d0455d20978d4ca/061f8e6afc6c4ac7122f35bcfdc999b494023691/README.yaml b/Simulations/1a0/277/1a02776e006c5309008deeb88d0455d20978d4ca/061f8e6afc6c4ac7122f35bcfdc999b494023691/README.yaml index e89ed7a278..5aaf548baf 100644 --- a/Simulations/1a0/277/1a02776e006c5309008deeb88d0455d20978d4ca/061f8e6afc6c4ac7122f35bcfdc999b494023691/README.yaml +++ b/Simulations/1a0/277/1a02776e006c5309008deeb88d0455d20978d4ca/061f8e6afc6c4ac7122f35bcfdc999b494023691/README.yaml @@ -56,9 +56,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 437 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL/POPS (61:14:13:12) bilayer at 298 K (CHARMM36, GROMACS, 200 ns) [NMRlipids simulation 437] + name: Molecular dynamics trajectory of a POPC/CLA/CAL/POPS (61:14:13:12) bilayer + at 298 K (CHARMM36, GROMACS, 200 ns) [NMRlipids simulation 437] alternateName: 250POPC_50POPS_53CAL_56CLA_298K_73529Atoms - description: Molecular dynamics trajectory of a lipid bilayer of 250 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 61 mol%), 56 CLA (14 mol%), 53 CAL (13 mol%) and 50 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 12 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for 200 ns (73529 atoms). Deposited as NMRlipids Databank simulation 437 and available from https://doi.org/10.5281/zenodo.2542176. + description: Molecular dynamics trajectory of a lipid bilayer of 250 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 61 mol%), 56 CLA (14 mol%), 53 CAL (13 mol%) and 50 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, + 12 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for 200 ns (73529 atoms). + Deposited as NMRlipids Databank simulation 437 and available from https://doi.org/10.5281/zenodo.2542176. sameAs: https://doi.org/10.5281/zenodo.2542176 datePublished: '2019-01-14' license: diff --git a/Simulations/1a0/b6e/1a0b6e4b7e964cb51a2166ffdec28a9628a66213/4cc5c88c00d71f3431d40ab68d66e10039b03155/README.yaml b/Simulations/1a0/b6e/1a0b6e4b7e964cb51a2166ffdec28a9628a66213/4cc5c88c00d71f3431d40ab68d66e10039b03155/README.yaml index 28eced49ab..fff27f618f 100644 --- a/Simulations/1a0/b6e/1a0b6e4b7e964cb51a2166ffdec28a9628a66213/4cc5c88c00d71f3431d40ab68d66e10039b03155/README.yaml +++ b/Simulations/1a0/b6e/1a0b6e4b7e964cb51a2166ffdec28a9628a66213/4cc5c88c00d71f3431d40ab68d66e10039b03155/README.yaml @@ -43,9 +43,12 @@ SOFTWARE: gromacs DIR_WRK: /usr/home/bort/Databank ID: 438 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC bilayer at 325 K (CHARMM36, GROMACS 5.0.4, 500 ns) [NMRlipids simulation 438] + name: Molecular dynamics trajectory of a DPPC bilayer at 325 K (CHARMM36, GROMACS + 5.0.4, 500 ns) [NMRlipids simulation 438] alternateName: 72DPPC_2880SOL_325K - description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) at 325 K. Simulated with CHARMM36 in GROMACS 5.0.4 for 500 ns (18000 atoms). Deposited as NMRlipids Databank simulation 438 and available from https://doi.org/10.5281/zenodo.1009607. + description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) + at 325 K. Simulated with CHARMM36 in GROMACS 5.0.4 for 500 ns (18000 atoms). Deposited + as NMRlipids Databank simulation 438 and available from https://doi.org/10.5281/zenodo.1009607. sameAs: https://doi.org/10.5281/zenodo.1009607 datePublished: '2017-10-12' license: @@ -140,7 +143,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1009607 identifier: 10.5281/zenodo.1009607 url: https://doi.org/10.5281/zenodo.1009607 - name: Set Simulations Small Pure Bilayers (72 Lipids) Using Charmm36 Ff In Gromacs (Dppc, Popc) + name: Set Simulations Small Pure Bilayers (72 Lipids) Using Charmm36 Ff In Gromacs + (Dppc, Popc) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/1a3/09f/1a309f2e399c5a6ab26cad208a8b8d273a985318/3f267aa1bc067d00566db164a4edc359b33c1246/README.yaml b/Simulations/1a3/09f/1a309f2e399c5a6ab26cad208a8b8d273a985318/3f267aa1bc067d00566db164a4edc359b33c1246/README.yaml index af1d5f774e..7fd5e7fc1a 100644 --- a/Simulations/1a3/09f/1a309f2e399c5a6ab26cad208a8b8d273a985318/3f267aa1bc067d00566db164a4edc359b33c1246/README.yaml +++ b/Simulations/1a3/09f/1a309f2e399c5a6ab26cad208a8b8d273a985318/3f267aa1bc067d00566db164a4edc359b33c1246/README.yaml @@ -51,9 +51,13 @@ EXPERIMENT: GB3: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD/GB3 (75:11:11:4) bilayer at 310 K (CHARMM36m, GROMACS 2019.4/2020, 7245 ns) [NMRlipids simulation 852] + name: Molecular dynamics trajectory of a POPC/CLA/SOD/GB3 (75:11:11:4) bilayer at + 310 K (CHARMM36m, GROMACS 2019.4/2020, 7245 ns) [NMRlipids simulation 852] alternateName: POPC:Gb3_run3(95:5 mol:mol) - description: Molecular dynamics trajectory of a lipid bilayer of 190 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 75 mol%), 27 CLA (11 mol%), 27 SOD (11 mol%) and 10 GB3 (Gb3(d18:1/24:0), 4 mol%) at 310 K. Simulated with CHARMM36m in GROMACS 2019.4/2020 for 7245 ns (74381 atoms). Deposited as NMRlipids Databank simulation 852 and available from https://doi.org/10.5281/zenodo.8335207. + description: Molecular dynamics trajectory of a lipid bilayer of 190 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 75 mol%), 27 CLA (11 mol%), 27 SOD (11 mol%) and 10 GB3 (Gb3(d18:1/24:0), 4 mol%) + at 310 K. Simulated with CHARMM36m in GROMACS 2019.4/2020 for 7245 ns (74381 atoms). + Deposited as NMRlipids Databank simulation 852 and available from https://doi.org/10.5281/zenodo.8335207. sameAs: https://doi.org/10.5281/zenodo.8335207 datePublished: '2024-02-08' publisher: Zenodo diff --git a/Simulations/1ad/14d/1ad14db0e1399314b67b24b153f0939b458fc807/94465ee5b92af8fc395f602ad8769567fc1e9c3d/README.yaml b/Simulations/1ad/14d/1ad14db0e1399314b67b24b153f0939b458fc807/94465ee5b92af8fc395f602ad8769567fc1e9c3d/README.yaml index ce5e160669..1ce471ac80 100644 --- a/Simulations/1ad/14d/1ad14db0e1399314b67b24b153f0939b458fc807/94465ee5b92af8fc395f602ad8769567fc1e9c3d/README.yaml +++ b/Simulations/1ad/14d/1ad14db0e1399314b67b24b153f0939b458fc807/94465ee5b92af8fc395f602ad8769567fc1e9c3d/README.yaml @@ -44,9 +44,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 394 bioschema_properties: - name: Molecular dynamics trajectory of a DOPC bilayer at 333.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 394] + name: Molecular dynamics trajectory of a DOPC bilayer at 333.15 K (CHARMM36, GROMACS, + 1001 ns) [NMRlipids simulation 394] alternateName: 1024DOPC_51200SOL_333K - description: Molecular dynamics trajectory of a lipid bilayer of 1024 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (294912 atoms). Deposited as NMRlipids Databank simulation 394 and available from https://doi.org/10.5281/zenodo.6943413. + description: Molecular dynamics trajectory of a lipid bilayer of 1024 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) + at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (294912 atoms). Deposited + as NMRlipids Databank simulation 394 and available from https://doi.org/10.5281/zenodo.6943413. sameAs: https://doi.org/10.5281/zenodo.6943413 datePublished: '2022-07-30' license: @@ -134,7 +137,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.6943413 identifier: 10.5281/zenodo.6943413 url: https://doi.org/10.5281/zenodo.6943413 - name: Simulations of different single-component bilayers, three different system sizes + name: Simulations of different single-component bilayers, three different system + sizes publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/1af/494/1af49498ed5c1f3f8f38daeb37dcd2243c79391e/bb80b1bf80b95dc4fdf84bc17c78e8f7a0000b81/DPPC_FragmentQuality.json b/Simulations/1af/494/1af49498ed5c1f3f8f38daeb37dcd2243c79391e/bb80b1bf80b95dc4fdf84bc17c78e8f7a0000b81/DPPC_FragmentQuality.json new file mode 100644 index 0000000000..64e3ab489b --- /dev/null +++ b/Simulations/1af/494/1af49498ed5c1f3f8f38daeb37dcd2243c79391e/bb80b1bf80b95dc4fdf84bc17c78e8f7a0000b81/DPPC_FragmentQuality.json @@ -0,0 +1 @@ +{"sn-1": NaN, "sn-2": NaN, "headgroup": 0.6561, "total": 0.6561} \ No newline at end of file diff --git a/Simulations/1af/494/1af49498ed5c1f3f8f38daeb37dcd2243c79391e/bb80b1bf80b95dc4fdf84bc17c78e8f7a0000b81/DPPC_OrderParameters_quality.json b/Simulations/1af/494/1af49498ed5c1f3f8f38daeb37dcd2243c79391e/bb80b1bf80b95dc4fdf84bc17c78e8f7a0000b81/DPPC_OrderParameters_quality.json new file mode 100644 index 0000000000..b2c28a9b73 --- /dev/null +++ b/Simulations/1af/494/1af49498ed5c1f3f8f38daeb37dcd2243c79391e/bb80b1bf80b95dc4fdf84bc17c78e8f7a0000b81/DPPC_OrderParameters_quality.json @@ -0,0 +1,84 @@ +{ + "10.1021/bi00687a021/1": { + "M_G1C10_M M_G1C10H1_M": NaN, + "M_G1C10_M M_G1C10H2_M": NaN, + "M_G1C11_M M_G1C11H1_M": NaN, + "M_G1C11_M M_G1C11H2_M": NaN, + "M_G1C12_M M_G1C12H1_M": NaN, + "M_G1C12_M M_G1C12H2_M": NaN, + "M_G1C13_M M_G1C13H1_M": 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"M_G2C13_M M_G2C13H1_M": NaN, + "M_G2C13_M M_G2C13H2_M": NaN, + "M_G2C14_M M_G2C14H1_M": NaN, + "M_G2C14_M M_G2C14H2_M": NaN, + "M_G2C15_M M_G2C15H1_M": NaN, + "M_G2C15_M M_G2C15H2_M": NaN, + "M_G2C16_M M_G2C16H1_M": NaN, + "M_G2C16_M M_G2C16H2_M": NaN, + "M_G2C17_M M_G2C17H1_M": NaN, + "M_G2C17_M M_G2C17H2_M": NaN, + "M_G2C17_M M_G2C17H3_M": NaN, + "M_G2C3_M M_G2C3H1_M": NaN, + "M_G2C3_M M_G2C3H2_M": NaN, + "M_G2C4_M M_G2C4H1_M": NaN, + "M_G2C4_M M_G2C4H2_M": NaN, + "M_G2C5_M M_G2C5H1_M": NaN, + "M_G2C5_M M_G2C5H2_M": NaN, + "M_G2C6_M M_G2C6H1_M": NaN, + "M_G2C6_M M_G2C6H2_M": NaN, + "M_G2C7_M M_G2C7H1_M": NaN, + "M_G2C7_M M_G2C7H2_M": NaN, + "M_G2C8_M M_G2C8H1_M": NaN, + "M_G2C8_M M_G2C8H2_M": NaN, + "M_G2C9_M M_G2C9H1_M": NaN, + "M_G2C9_M M_G2C9H2_M": NaN, + "M_G2_M M_G2H1_M": NaN, + "M_G3C4_M M_G3C4H1_M": 0.0225, + "M_G3C4_M M_G3C4H2_M": 0.0281, + "M_G3C5_M M_G3C5H1_M": 0.9463, + "M_G3C5_M M_G3C5H2_M": 0.9241, + "M_G3N6C1_M M_G3N6C1H1_M": 0.9897, + "M_G3N6C1_M M_G3N6C1H2_M": 0.9879, + "M_G3N6C1_M M_G3N6C1H3_M": 0.9885, + "M_G3N6C2_M M_G3N6C2H1_M": 0.9883, + "M_G3N6C2_M M_G3N6C2H2_M": 0.988, + "M_G3N6C2_M M_G3N6C2H3_M": 0.9889, + "M_G3N6C3_M M_G3N6C3H1_M": 0.9884, + "M_G3N6C3_M M_G3N6C3H2_M": 0.9889, + "M_G3N6C3_M M_G3N6C3H3_M": 0.9877, + "M_G3_M M_G3H1_M": 0.0242, + "M_G3_M M_G3H2_M": 0.9678 + } +} \ No newline at end of file diff --git a/Simulations/1af/494/1af49498ed5c1f3f8f38daeb37dcd2243c79391e/bb80b1bf80b95dc4fdf84bc17c78e8f7a0000b81/FormFactorQuality.json b/Simulations/1af/494/1af49498ed5c1f3f8f38daeb37dcd2243c79391e/bb80b1bf80b95dc4fdf84bc17c78e8f7a0000b81/FormFactorQuality.json new file mode 100644 index 0000000000..988a264fe1 --- /dev/null +++ b/Simulations/1af/494/1af49498ed5c1f3f8f38daeb37dcd2243c79391e/bb80b1bf80b95dc4fdf84bc17c78e8f7a0000b81/FormFactorQuality.json @@ -0,0 +1 @@ +[0.4128, 91.8733] \ No newline at end of file diff --git a/Simulations/1af/494/1af49498ed5c1f3f8f38daeb37dcd2243c79391e/bb80b1bf80b95dc4fdf84bc17c78e8f7a0000b81/README.yaml b/Simulations/1af/494/1af49498ed5c1f3f8f38daeb37dcd2243c79391e/bb80b1bf80b95dc4fdf84bc17c78e8f7a0000b81/README.yaml index bef321f3f9..b44e819a52 100644 --- a/Simulations/1af/494/1af49498ed5c1f3f8f38daeb37dcd2243c79391e/bb80b1bf80b95dc4fdf84bc17c78e8f7a0000b81/README.yaml +++ b/Simulations/1af/494/1af49498ed5c1f3f8f38daeb37dcd2243c79391e/bb80b1bf80b95dc4fdf84bc17c78e8f7a0000b81/README.yaml @@ -39,3 +39,9 @@ NUMBER_OF_ATOMS: 53000 DATEOFRUNNING: 15/09/2026 TYPEOFSYSTEM: lipid bilayer ID: 931 +EXPERIMENT: + ORDERPARAMETER: + DPPC: + - 10.1021/bi00687a021/1 + FORMFACTOR: + - 10.1016/j.bbamem.2011.07.022/4 diff --git a/Simulations/1af/494/1af49498ed5c1f3f8f38daeb37dcd2243c79391e/bb80b1bf80b95dc4fdf84bc17c78e8f7a0000b81/SYSTEM_quality.json b/Simulations/1af/494/1af49498ed5c1f3f8f38daeb37dcd2243c79391e/bb80b1bf80b95dc4fdf84bc17c78e8f7a0000b81/SYSTEM_quality.json new file mode 100644 index 0000000000..b28ff5bae8 --- /dev/null +++ b/Simulations/1af/494/1af49498ed5c1f3f8f38daeb37dcd2243c79391e/bb80b1bf80b95dc4fdf84bc17c78e8f7a0000b81/SYSTEM_quality.json @@ -0,0 +1 @@ +{"headgroup": 0.6561, "tails": 0.0, "total": 0.6561} \ No newline at end of file diff --git a/Simulations/1af/8f6/1af8f6529627bed6a08027160f933a8ac5c5b86b/986ca46503349f7466c65e0dc3e2471376de1a28/README.yaml b/Simulations/1af/8f6/1af8f6529627bed6a08027160f933a8ac5c5b86b/986ca46503349f7466c65e0dc3e2471376de1a28/README.yaml index d715d40a91..a6ca33d7b6 100644 --- a/Simulations/1af/8f6/1af8f6529627bed6a08027160f933a8ac5c5b86b/986ca46503349f7466c65e0dc3e2471376de1a28/README.yaml +++ b/Simulations/1af/8f6/1af8f6529627bed6a08027160f933a8ac5c5b86b/986ca46503349f7466c65e0dc3e2471376de1a28/README.yaml @@ -57,9 +57,14 @@ DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 180 AUTHORS_CONTACT: Kiirikki, M. Anne; Ollila O. H. Samuli bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/POPG/SOD/CAL (52:14:13:13:7) bilayer at 298 K (CHARMM36, GROMACS, 300 ns) [NMRlipids simulation 180] + name: Molecular dynamics trajectory of a POPC/CLA/POPG/SOD/CAL (52:14:13:13:7) bilayer + at 298 K (CHARMM36, GROMACS, 300 ns) [NMRlipids simulation 180] alternateName: POPC:POPG(4:1)+0.1MCaCl_T298K - description: Molecular dynamics trajectory of a lipid bilayer of 350 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 52 mol%), 94 CLA (14 mol%), 88 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 13 mol%), 88 SOD (13 mol%) and 47 CAL (7 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for 300 ns (137145 atoms). Deposited as NMRlipids Databank simulation 180 and available from https://doi.org/10.5281/zenodo.3997019. + description: Molecular dynamics trajectory of a lipid bilayer of 350 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 52 mol%), 94 CLA (14 mol%), 88 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, + 13 mol%), 88 SOD (13 mol%) and 47 CAL (7 mol%) at 298 K. Simulated with CHARMM36 + in GROMACS for 300 ns (137145 atoms). Deposited as NMRlipids Databank simulation + 180 and available from https://doi.org/10.5281/zenodo.3997019. sameAs: https://doi.org/10.5281/zenodo.3997019 datePublished: '2020-08-24' license: @@ -149,7 +154,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3997019 identifier: 10.5281/zenodo.3997019 url: https://doi.org/10.5281/zenodo.3997019 - name: POPC:POPG 4:1 MD simulation with CHARMM36 in 0.1 M CaCL2 solution with Na+ counter ions + name: POPC:POPG 4:1 MD simulation with CHARMM36 in 0.1 M CaCL2 solution with Na+ + counter ions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/1b2/1b8/1b21b86ce63406320f7b11136b7382d5b27e8ac6/d3dffede22d2141bd77587752021c6e9feb18e44/README.yaml b/Simulations/1b2/1b8/1b21b86ce63406320f7b11136b7382d5b27e8ac6/d3dffede22d2141bd77587752021c6e9feb18e44/README.yaml index 631657bb77..4aabe082a6 100644 --- a/Simulations/1b2/1b8/1b21b86ce63406320f7b11136b7382d5b27e8ac6/d3dffede22d2141bd77587752021c6e9feb18e44/README.yaml +++ b/Simulations/1b2/1b8/1b21b86ce63406320f7b11136b7382d5b27e8ac6/d3dffede22d2141bd77587752021c6e9feb18e44/README.yaml @@ -44,9 +44,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 6 bioschema_properties: - name: Molecular dynamics trajectory of a DLIPC bilayer at 333.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 6] + name: Molecular dynamics trajectory of a DLIPC bilayer at 333.15 K (CHARMM36, GROMACS, + 1001 ns) [NMRlipids simulation 6] alternateName: 256DLIPC_12800SOL_333K - description: Molecular dynamics trajectory of a lipid bilayer of 256 DLIPC (1,2-dilinoleoyl-sn-glycero-3-phosphocholine) at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (72704 atoms). Deposited as NMRlipids Databank simulation 6 and available from https://doi.org/10.5281/zenodo.6943413. + description: Molecular dynamics trajectory of a lipid bilayer of 256 DLIPC (1,2-dilinoleoyl-sn-glycero-3-phosphocholine) + at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (72704 atoms). Deposited + as NMRlipids Databank simulation 6 and available from https://doi.org/10.5281/zenodo.6943413. sameAs: https://doi.org/10.5281/zenodo.6943413 datePublished: '2022-07-30' license: @@ -134,7 +137,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.6943413 identifier: 10.5281/zenodo.6943413 url: https://doi.org/10.5281/zenodo.6943413 - name: Simulations of different single-component bilayers, three different system sizes + name: Simulations of different single-component bilayers, three different system + sizes publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/1b2/6e6/1b26e6c750b4f39c37770422cd4d3c40240cf111/995bc873b811ca09c916b47784fa33bb9d793732/README.yaml b/Simulations/1b2/6e6/1b26e6c750b4f39c37770422cd4d3c40240cf111/995bc873b811ca09c916b47784fa33bb9d793732/README.yaml index d9991abd1f..7a5cdeecb7 100644 --- a/Simulations/1b2/6e6/1b26e6c750b4f39c37770422cd4d3c40240cf111/995bc873b811ca09c916b47784fa33bb9d793732/README.yaml +++ b/Simulations/1b2/6e6/1b26e6c750b4f39c37770422cd4d3c40240cf111/995bc873b811ca09c916b47784fa33bb9d793732/README.yaml @@ -44,9 +44,13 @@ TRJ: - - md-CHARMM36_10A-switch_POPS_v2_400-500ns_skip10.xtc ID: 5 bioschema_properties: - name: Molecular dynamics trajectory of a POPS/SOD (50:50) bilayer at 298 K (CHARMM36, GROMACS, 100 ns) [NMRlipids simulation 5] + name: Molecular dynamics trajectory of a POPS/SOD (50:50) bilayer at 298 K (CHARMM36, + GROMACS, 100 ns) [NMRlipids simulation 5] alternateName: POPS_298K - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 50 mol%) and 128 SOD (50 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for 100 ns (29824 atoms). Deposited as NMRlipids Databank simulation 5 and available from https://doi.org/10.5281/zenodo.1129415. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, + 50 mol%) and 128 SOD (50 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for + 100 ns (29824 atoms). Deposited as NMRlipids Databank simulation 5 and available + from https://doi.org/10.5281/zenodo.1129415. sameAs: https://doi.org/10.5281/zenodo.1129415 datePublished: '2017-12-24' license: diff --git a/Simulations/1b4/d5b/1b4d5b097a397af487bed5339ad72cefd4cd0986/e7764b21fa39e5153ae7c6371acdf3589dceee8f/README.yaml b/Simulations/1b4/d5b/1b4d5b097a397af487bed5339ad72cefd4cd0986/e7764b21fa39e5153ae7c6371acdf3589dceee8f/README.yaml index 8edafed20a..3c4b89d836 100644 --- a/Simulations/1b4/d5b/1b4d5b097a397af487bed5339ad72cefd4cd0986/e7764b21fa39e5153ae7c6371acdf3589dceee8f/README.yaml +++ b/Simulations/1b4/d5b/1b4d5b097a397af487bed5339ad72cefd4cd0986/e7764b21fa39e5153ae7c6371acdf3589dceee8f/README.yaml @@ -50,9 +50,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 391 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/CLA/SOD (82:9:9) bilayer at 338 K (CHARMM36, GROMACS 5.0.4, 500 ns) [NMRlipids simulation 391] + name: Molecular dynamics trajectory of a DPPC/CLA/SOD (82:9:9) bilayer at 338 K + (CHARMM36, GROMACS 5.0.4, 500 ns) [NMRlipids simulation 391] alternateName: DPPC_512_NaCl_150mM_325K_MEMB_338K - description: Molecular dynamics trajectory of a lipid bilayer of 512 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 82 mol%), 55 CLA (9 mol%) and 55 SOD (9 mol%) at 338 K. Simulated with CHARMM36 in GROMACS 5.0.4 for 500 ns (128110 atoms). Deposited as NMRlipids Databank simulation 391 and available from https://doi.org/10.5281/zenodo.1009027. + description: Molecular dynamics trajectory of a lipid bilayer of 512 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 82 mol%), 55 CLA (9 mol%) and 55 SOD (9 mol%) at 338 K. Simulated with CHARMM36 + in GROMACS 5.0.4 for 500 ns (128110 atoms). Deposited as NMRlipids Databank simulation + 391 and available from https://doi.org/10.5281/zenodo.1009027. sameAs: https://doi.org/10.5281/zenodo.1009027 datePublished: '2017-10-11' license: diff --git a/Simulations/1b5/fe7/1b5fe765d31ed81fcf5c139cf6ac6102f2995148/116afeefb5c67e782c5cc7bf9770fa6654a091fc/README.yaml b/Simulations/1b5/fe7/1b5fe765d31ed81fcf5c139cf6ac6102f2995148/116afeefb5c67e782c5cc7bf9770fa6654a091fc/README.yaml index fdb7f9d67c..dabbeb7297 100644 --- a/Simulations/1b5/fe7/1b5fe765d31ed81fcf5c139cf6ac6102f2995148/116afeefb5c67e782c5cc7bf9770fa6654a091fc/README.yaml +++ b/Simulations/1b5/fe7/1b5fe765d31ed81fcf5c139cf6ac6102f2995148/116afeefb5c67e782c5cc7bf9770fa6654a091fc/README.yaml @@ -50,9 +50,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 78 bioschema_properties: - name: Molecular dynamics trajectory of a CLA/POPC/CAL (41:39:20) bilayer at 303 K (CHARMM36, GROMACS 5.0.4, 100 ns) [NMRlipids simulation 78] + name: Molecular dynamics trajectory of a CLA/POPC/CAL (41:39:20) bilayer at 303 + K (CHARMM36, GROMACS 5.0.4, 100 ns) [NMRlipids simulation 78] alternateName: 128POPC_6400SOL_67CAL_134CLA_303K - description: Molecular dynamics trajectory of a lipid bilayer of 134 CLA (41 mol%), 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 39 mol%) and 67 CAL (20 mol%) at 303 K. Simulated with CHARMM36 in GROMACS 5.0.4 for 100 ns (36553 atoms). Deposited as NMRlipids Databank simulation 78 and available from https://doi.org/10.5281/zenodo.35160. + description: Molecular dynamics trajectory of a lipid bilayer of 134 CLA (41 mol%), + 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 39 mol%) and 67 CAL + (20 mol%) at 303 K. Simulated with CHARMM36 in GROMACS 5.0.4 for 100 ns (36553 + atoms). Deposited as NMRlipids Databank simulation 78 and available from https://doi.org/10.5281/zenodo.35160. sameAs: https://doi.org/10.5281/zenodo.35160 datePublished: '2015-12-10' license: diff --git a/Simulations/1c2/af7/1c2af781a6a8eb53691c1e62128ee4f62c7cec3a/a619cf1e310a2001b7a052ac4851169be5fe0e05/README.yaml b/Simulations/1c2/af7/1c2af781a6a8eb53691c1e62128ee4f62c7cec3a/a619cf1e310a2001b7a052ac4851169be5fe0e05/README.yaml index d6ad7cc44f..37917debf9 100644 --- a/Simulations/1c2/af7/1c2af781a6a8eb53691c1e62128ee4f62c7cec3a/a619cf1e310a2001b7a052ac4851169be5fe0e05/README.yaml +++ b/Simulations/1c2/af7/1c2af781a6a8eb53691c1e62128ee4f62c7cec3a/a619cf1e310a2001b7a052ac4851169be5fe0e05/README.yaml @@ -54,9 +54,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 530 bioschema_properties: - name: Molecular dynamics trajectory of a SOD/POPG/CLA (50:46:4) bilayer at 310 K (GROMOS-CKP-POPG-Tom_Piggot-v1, GROMACS 5.1.2, 100 ns) [NMRlipids simulation 530] + name: Molecular dynamics trajectory of a SOD/POPG/CLA (50:46:4) bilayer at 310 K + (GROMOS-CKP-POPG-Tom_Piggot-v1, GROMACS 5.1.2, 100 ns) [NMRlipids simulation 530] alternateName: 500POPG_25000SOL_549SOD_49CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 549 SOD (50 mol%), 500 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 46 mol%) and 49 CLA (4 mol%) at 310 K. Simulated with GROMOS-CKP-POPG-Tom_Piggot-v1 in GROMACS 5.1.2 for 100 ns (102098 atoms). Deposited as NMRlipids Databank simulation 530 and available from https://doi.org/10.5281/zenodo.3378992. + description: Molecular dynamics trajectory of a lipid bilayer of 549 SOD (50 mol%), + 500 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 46 mol%) and 49 CLA + (4 mol%) at 310 K. Simulated with GROMOS-CKP-POPG-Tom_Piggot-v1 in GROMACS 5.1.2 + for 100 ns (102098 atoms). Deposited as NMRlipids Databank simulation 530 and + available from https://doi.org/10.5281/zenodo.3378992. sameAs: https://doi.org/10.5281/zenodo.3378992 datePublished: '2019-02-19' license: diff --git a/Simulations/1c2/f06/1c2f06a9172359ef0e7599536966edff86498b63/1c2f06a9172359ef0e7599536966edff86498b63/README.yaml b/Simulations/1c2/f06/1c2f06a9172359ef0e7599536966edff86498b63/1c2f06a9172359ef0e7599536966edff86498b63/README.yaml index 71ad770926..ce16c10dfe 100644 --- a/Simulations/1c2/f06/1c2f06a9172359ef0e7599536966edff86498b63/1c2f06a9172359ef0e7599536966edff86498b63/README.yaml +++ b/Simulations/1c2/f06/1c2f06a9172359ef0e7599536966edff86498b63/1c2f06a9172359ef0e7599536966edff86498b63/README.yaml @@ -49,9 +49,13 @@ EXPERIMENT: POPC: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (51:33:16) bilayer at 303 K (Charmm-Drude polarizable, OPENMM, 220 ns) [NMRlipids simulation 757] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (51:33:16) bilayer at 303 + K (Charmm-Drude polarizable, OPENMM, 220 ns) [NMRlipids simulation 757] alternateName: POPC_350_CaCl2_CHARMMdrude2023_303K - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 51 mol%), 82 CLA (33 mol%) and 41 CAL (16 mol%) at 303 K. Simulated with Charmm-Drude polarizable in OPENMM for 220 ns (57078 atoms). Deposited as NMRlipids Databank simulation 757 and available from https://doi.org/10.5281/zenodo.8000065. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 51 mol%), 82 CLA (33 mol%) and 41 CAL (16 mol%) at 303 K. Simulated with Charmm-Drude + polarizable in OPENMM for 220 ns (57078 atoms). Deposited as NMRlipids Databank + simulation 757 and available from https://doi.org/10.5281/zenodo.8000065. sameAs: https://doi.org/10.5281/zenodo.8000065 datePublished: '2023-06-02' license: @@ -140,7 +144,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.8000065 identifier: 10.5281/zenodo.8000065 url: https://doi.org/10.5281/zenodo.8000065 - name: Pure POPC membrane simulations with 350 mM CaCl2 with the CHARMM-Drude2023 force field (OpenMM) + name: Pure POPC membrane simulations with 350 mM CaCl2 with the CHARMM-Drude2023 + force field (OpenMM) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/1c4/77d/1c477da411113327d1c0e43eea10b0f096031d45/35a315cecf0156381237417893bf6755b08ab3e8/README.yaml b/Simulations/1c4/77d/1c477da411113327d1c0e43eea10b0f096031d45/35a315cecf0156381237417893bf6755b08ab3e8/README.yaml index ad6a7f1881..614c290435 100644 --- a/Simulations/1c4/77d/1c477da411113327d1c0e43eea10b0f096031d45/35a315cecf0156381237417893bf6755b08ab3e8/README.yaml +++ b/Simulations/1c4/77d/1c477da411113327d1c0e43eea10b0f096031d45/35a315cecf0156381237417893bf6755b08ab3e8/README.yaml @@ -60,9 +60,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 418 bioschema_properties: - name: Molecular dynamics trajectory of a CLA/CAL/POPC/POPG/SOD (49:24:18:5:5) bilayer at 298 K (Lipid17, GROMACS, 200 ns) [NMRlipids simulation 418] + name: Molecular dynamics trajectory of a CLA/CAL/POPC/POPG/SOD (49:24:18:5:5) bilayer + at 298 K (Lipid17, GROMACS, 200 ns) [NMRlipids simulation 418] alternateName: 350POPC_88POPG_24840SOL_475CAL_950CLA_88SOD_298K - description: Molecular dynamics trajectory of a lipid bilayer of 950 CLA (49 mol%), 475 CAL (24 mol%), 350 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 18 mol%), 88 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 5 mol%) and 88 SOD (5 mol%) at 298 K. Simulated with Lipid17 in GROMACS for 200 ns (134109 atoms). Deposited as NMRlipids Databank simulation 418 and available from https://doi.org/10.5281/zenodo.3874378. + description: Molecular dynamics trajectory of a lipid bilayer of 950 CLA (49 mol%), + 475 CAL (24 mol%), 350 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 18 mol%), 88 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 5 mol%) + and 88 SOD (5 mol%) at 298 K. Simulated with Lipid17 in GROMACS for 200 ns (134109 + atoms). Deposited as NMRlipids Databank simulation 418 and available from https://doi.org/10.5281/zenodo.3874378. sameAs: https://doi.org/10.5281/zenodo.3874378 datePublished: '2019-10-23' license: @@ -154,7 +159,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3874378 identifier: 10.5281/zenodo.3874378 url: https://doi.org/10.5281/zenodo.3874378 - name: LIPID17 POPC-POPG 80:20 MD simulation, Na+ counterions and 1000mM CaCl2, 298K + name: LIPID17 POPC-POPG 80:20 MD simulation, Na+ counterions and 1000mM CaCl2, + 298K publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/1c6/213/1c62137370ddb732012f431ecd647f8490b243f1/19e060bb4e007489a0da5936e99d20c97097ffd0/README.yaml b/Simulations/1c6/213/1c62137370ddb732012f431ecd647f8490b243f1/19e060bb4e007489a0da5936e99d20c97097ffd0/README.yaml index 0c8dd012a5..aac3ebbd64 100644 --- a/Simulations/1c6/213/1c62137370ddb732012f431ecd647f8490b243f1/19e060bb4e007489a0da5936e99d20c97097ffd0/README.yaml +++ b/Simulations/1c6/213/1c62137370ddb732012f431ecd647f8490b243f1/19e060bb4e007489a0da5936e99d20c97097ffd0/README.yaml @@ -63,9 +63,16 @@ EXPERIMENT: FORMFACTOR: [] ID: 25 bioschema_properties: - name: Molecular dynamics trajectory of a CLA/POPC/CAL/POPS/SOD (39:30:19:6:6) bilayer at 298 K (ECC-lipids, SPC/E water model, ECC-ions, GROMACS 2018.0, 823 ns) [NMRlipids simulation 25] + name: Molecular dynamics trajectory of a CLA/POPC/CAL/POPS/SOD (39:30:19:6:6) bilayer + at 298 K (ECC-lipids, SPC/E water model, ECC-ions, GROMACS 2018.0, 823 ns) [NMRlipids + simulation 25] alternateName: 12POPS_60POPC_3483SOL_39CAL_78CLA_12SOD_298K - description: Molecular dynamics trajectory of a lipid bilayer of 78 CLA (39 mol%), 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 30 mol%), 39 CAL (19 mol%), 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 6 mol%) and 12 SOD (6 mol%) at 298 K. Simulated with ECC-lipids, SPC/E water model, ECC-ions in GROMACS 2018.0 for 823 ns (20142 atoms). Deposited as NMRlipids Databank simulation 25 and available from https://doi.org/10.5281/zenodo.1488102. + description: Molecular dynamics trajectory of a lipid bilayer of 78 CLA (39 mol%), + 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 30 mol%), 39 CAL (19 + mol%), 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 6 mol%) and + 12 SOD (6 mol%) at 298 K. Simulated with ECC-lipids, SPC/E water model, ECC-ions + in GROMACS 2018.0 for 823 ns (20142 atoms). Deposited as NMRlipids Databank simulation + 25 and available from https://doi.org/10.5281/zenodo.1488102. sameAs: https://doi.org/10.5281/zenodo.1488102 datePublished: '2018-11-14' license: @@ -158,7 +165,9 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1488102 identifier: 10.5281/zenodo.1488102 url: https://doi.org/10.5281/zenodo.1488102 - name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS (5:1) with ECC-lipids force field, and Na+ (K+) counterions at various CaCl2 additional concentrations + name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS + (5:1) with ECC-lipids force field, and Na+ (K+) counterions at various CaCl2 + additional concentrations publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/1cc/c95/1ccc95a2fbe4eb6dc3442672820449a667b6c809/fa35f5627cf4ebe0a9d248fc0ff3b5d474181b8c/README.yaml b/Simulations/1cc/c95/1ccc95a2fbe4eb6dc3442672820449a667b6c809/fa35f5627cf4ebe0a9d248fc0ff3b5d474181b8c/README.yaml index 4efc41ad03..666b04eeb0 100644 --- a/Simulations/1cc/c95/1ccc95a2fbe4eb6dc3442672820449a667b6c809/fa35f5627cf4ebe0a9d248fc0ff3b5d474181b8c/README.yaml +++ b/Simulations/1cc/c95/1ccc95a2fbe4eb6dc3442672820449a667b6c809/fa35f5627cf4ebe0a9d248fc0ff3b5d474181b8c/README.yaml @@ -60,9 +60,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 182 bioschema_properties: - name: Molecular dynamics trajectory of a CLA/CAL/POPC/POPG/SOD (53:26:7:7:7) bilayer at 298 K (Lipid17, GROMACS, 200 ns) [NMRlipids simulation 182] + name: Molecular dynamics trajectory of a CLA/CAL/POPC/POPG/SOD (53:26:7:7:7) bilayer + at 298 K (Lipid17, GROMACS, 200 ns) [NMRlipids simulation 182] alternateName: 150POPC_150POPG_29865SOL_569CAL_1138CLA_150SOD_298K - description: Molecular dynamics trajectory of a lipid bilayer of 1138 CLA (53 mol%), 569 CAL (26 mol%), 150 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 7 mol%), 150 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 7 mol%) and 150 SOD (7 mol%) at 298 K. Simulated with Lipid17 in GROMACS for 200 ns (130602 atoms). Deposited as NMRlipids Databank simulation 182 and available from https://doi.org/10.5281/zenodo.3864993. + description: Molecular dynamics trajectory of a lipid bilayer of 1138 CLA (53 mol%), + 569 CAL (26 mol%), 150 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 7 mol%), 150 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 7 mol%) + and 150 SOD (7 mol%) at 298 K. Simulated with Lipid17 in GROMACS for 200 ns (130602 + atoms). Deposited as NMRlipids Databank simulation 182 and available from https://doi.org/10.5281/zenodo.3864993. sameAs: https://doi.org/10.5281/zenodo.3864993 datePublished: '2019-10-28' license: @@ -154,7 +159,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3864993 identifier: 10.5281/zenodo.3864993 url: https://doi.org/10.5281/zenodo.3864993 - name: LIPID17 POPC-POPG 50:50 MD simulation, Na+ counterions and 1000mM CaCl2, 298K + name: LIPID17 POPC-POPG 50:50 MD simulation, Na+ counterions and 1000mM CaCl2, + 298K publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/1cf/5b8/1cf5b86ae03a9c69a520d6aa84efb1488b37096f/4e2199958d6361d53df071b10e33836d6761fe73/README.yaml b/Simulations/1cf/5b8/1cf5b86ae03a9c69a520d6aa84efb1488b37096f/4e2199958d6361d53df071b10e33836d6761fe73/README.yaml index bbd9ad6ea5..f61b742229 100644 --- a/Simulations/1cf/5b8/1cf5b86ae03a9c69a520d6aa84efb1488b37096f/4e2199958d6361d53df071b10e33836d6761fe73/README.yaml +++ b/Simulations/1cf/5b8/1cf5b86ae03a9c69a520d6aa84efb1488b37096f/4e2199958d6361d53df071b10e33836d6761fe73/README.yaml @@ -41,9 +41,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 606 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 298 K (MacRog, GROMACS 4.5.5, 50 ns) [NMRlipids simulation 606] + name: Molecular dynamics trajectory of a POPC bilayer at 298 K (MacRog, GROMACS + 4.5.5, 50 ns) [NMRlipids simulation 606] alternateName: 288POPC_5760SOL_298K - description: Molecular dynamics trajectory of a lipid bilayer of 288 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 298 K. Simulated with MacRog in GROMACS 4.5.5 for 50 ns (55872 atoms). Deposited as NMRlipids Databank simulation 606 and available from https://doi.org/10.5281/zenodo.13498. + description: Molecular dynamics trajectory of a lipid bilayer of 288 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 298 K. Simulated with MacRog in GROMACS 4.5.5 for 50 ns (55872 atoms). Deposited + as NMRlipids Databank simulation 606 and available from https://doi.org/10.5281/zenodo.13498. sameAs: https://doi.org/10.5281/zenodo.13498 datePublished: '2014-12-30' license: diff --git a/Simulations/1d0/5fe/1d05fe97e0d99fc700ba25dd4f28b8f75758fb3a/9743c5e991c6a9291162166e57dff7183f6a3dcf/README.yaml b/Simulations/1d0/5fe/1d05fe97e0d99fc700ba25dd4f28b8f75758fb3a/9743c5e991c6a9291162166e57dff7183f6a3dcf/README.yaml index ed4eac93a5..c17fdd7703 100644 --- a/Simulations/1d0/5fe/1d05fe97e0d99fc700ba25dd4f28b8f75758fb3a/9743c5e991c6a9291162166e57dff7183f6a3dcf/README.yaml +++ b/Simulations/1d0/5fe/1d05fe97e0d99fc700ba25dd4f28b8f75758fb3a/9743c5e991c6a9291162166e57dff7183f6a3dcf/README.yaml @@ -48,9 +48,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 869 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (56:22:22) bilayer at 300 K (OPLS3e, GROMACS Desmond of Schrödinger 2019-4, 900 ns) [NMRlipids simulation 869] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (56:22:22) bilayer at 300 + K (OPLS3e, GROMACS Desmond of Schrödinger 2019-4, 900 ns) [NMRlipids simulation + 869] alternateName: POPC, 44 w/l, 300 K, 0.5 M NaCl - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 56 mol%), 80 CLA (22 mol%) and 80 SOD (22 mol%) at 300 K. Simulated with OPLS3e in GROMACS Desmond of Schrödinger 2019-4 for 900 ns (53600 atoms). Deposited as NMRlipids Databank simulation 869 and available from https://doi.org/10.5281/zenodo.10200685. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 56 mol%), 80 CLA (22 mol%) and 80 SOD (22 mol%) at 300 K. Simulated with OPLS3e + in GROMACS Desmond of Schrödinger 2019-4 for 900 ns (53600 atoms). Deposited as + NMRlipids Databank simulation 869 and available from https://doi.org/10.5281/zenodo.10200685. sameAs: https://doi.org/10.5281/zenodo.10200685 datePublished: '2022' license: @@ -141,7 +146,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.10200685 identifier: 10.5281/zenodo.10200685 url: https://doi.org/10.5281/zenodo.10200685 - name: MD simulation of POPC bilayer with OPLS3e force field, 500 mM NaCl part 1 + name: MD simulation of POPC bilayer with OPLS3e force field, 500 mM NaCl part + 1 publisher: Zenodo _source: api: datacite diff --git a/Simulations/1d0/c13/1d0c13e8ed39cf959867c137b7f20aa08060885c/c639c6a4ea07e111c9c21446c45fb0282798550f/README.yaml b/Simulations/1d0/c13/1d0c13e8ed39cf959867c137b7f20aa08060885c/c639c6a4ea07e111c9c21446c45fb0282798550f/README.yaml index 787a9dd0d7..56af304d2e 100644 --- a/Simulations/1d0/c13/1d0c13e8ed39cf959867c137b7f20aa08060885c/c639c6a4ea07e111c9c21446c45fb0282798550f/README.yaml +++ b/Simulations/1d0/c13/1d0c13e8ed39cf959867c137b7f20aa08060885c/c639c6a4ea07e111c9c21446c45fb0282798550f/README.yaml @@ -46,9 +46,12 @@ EXPERIMENT: - 10.1016/j.bbamem.2011.07.022/10 ID: 254 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC bilayer at 333.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 254] + name: Molecular dynamics trajectory of a DPPC bilayer at 333.15 K (CHARMM36, GROMACS, + 1001 ns) [NMRlipids simulation 254] alternateName: 1024DPPC_51200SOL_333K - description: Molecular dynamics trajectory of a lipid bilayer of 1024 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (286720 atoms). Deposited as NMRlipids Databank simulation 254 and available from https://doi.org/10.5281/zenodo.6943413. + description: Molecular dynamics trajectory of a lipid bilayer of 1024 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) + at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (286720 atoms). Deposited + as NMRlipids Databank simulation 254 and available from https://doi.org/10.5281/zenodo.6943413. sameAs: https://doi.org/10.5281/zenodo.6943413 datePublished: '2022-07-30' license: @@ -139,7 +142,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.6943413 identifier: 10.5281/zenodo.6943413 url: https://doi.org/10.5281/zenodo.6943413 - name: Simulations of different single-component bilayers, three different system sizes + name: Simulations of different single-component bilayers, three different system + sizes publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/1d8/4fd/1d84fd1f2981492c978058d35c31876f932def55/4e032d4b41fe6a7d69a7ec3920115b404c97df03/README.yaml b/Simulations/1d8/4fd/1d84fd1f2981492c978058d35c31876f932def55/4e032d4b41fe6a7d69a7ec3920115b404c97df03/README.yaml index ebb3cc4dae..3e9e06c7d4 100644 --- a/Simulations/1d8/4fd/1d84fd1f2981492c978058d35c31876f932def55/4e032d4b41fe6a7d69a7ec3920115b404c97df03/README.yaml +++ b/Simulations/1d8/4fd/1d84fd1f2981492c978058d35c31876f932def55/4e032d4b41fe6a7d69a7ec3920115b404c97df03/README.yaml @@ -48,9 +48,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 250 bioschema_properties: - name: Molecular dynamics trajectory of a CHOL/POPC (50:50) bilayer at 303 K (Slipids, GROMACS 2020.1, 1200 ns) [NMRlipids simulation 250] + name: Molecular dynamics trajectory of a CHOL/POPC (50:50) bilayer at 303 K (Slipids, + GROMACS 2020.1, 1200 ns) [NMRlipids simulation 250] alternateName: 122CHOL_122POPC_9760SOL_303K - description: Molecular dynamics trajectory of a lipid bilayer of 122 CHOL (cholesterol, 50 mol%) and 122 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 50 mol%) at 303 K. Simulated with Slipids in GROMACS 2020.1 for 1200 ns (54656 atoms). Deposited as NMRlipids Databank simulation 250 and available from https://doi.org/10.5281/zenodo.4349753. + description: Molecular dynamics trajectory of a lipid bilayer of 122 CHOL (cholesterol, + 50 mol%) and 122 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 50 mol%) + at 303 K. Simulated with Slipids in GROMACS 2020.1 for 1200 ns (54656 atoms). + Deposited as NMRlipids Databank simulation 250 and available from https://doi.org/10.5281/zenodo.4349753. sameAs: https://doi.org/10.5281/zenodo.4349753 datePublished: '2020-12-18' license: diff --git a/Simulations/1d9/d4f/1d9d4f9f33055b16b3b8a438fac7013ae39cc712/02048411dc25c6cb5a072f50ac939ad53b399d1c/README.yaml b/Simulations/1d9/d4f/1d9d4f9f33055b16b3b8a438fac7013ae39cc712/02048411dc25c6cb5a072f50ac939ad53b399d1c/README.yaml index c7f994e327..1253596d2c 100644 --- a/Simulations/1d9/d4f/1d9d4f9f33055b16b3b8a438fac7013ae39cc712/02048411dc25c6cb5a072f50ac939ad53b399d1c/README.yaml +++ b/Simulations/1d9/d4f/1d9d4f9f33055b16b3b8a438fac7013ae39cc712/02048411dc25c6cb5a072f50ac939ad53b399d1c/README.yaml @@ -57,9 +57,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 604 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL/CHOL (45:33:17:5) bilayer at 310 K (Slipids with ECC-scaled ions (Kohagen), GROMACS 4.6, 600 ns) [NMRlipids simulation 604] + name: Molecular dynamics trajectory of a POPC/CLA/CAL/CHOL (45:33:17:5) bilayer + at 310 K (Slipids with ECC-scaled ions (Kohagen), GROMACS 4.6, 600 ns) [NMRlipids + simulation 604] alternateName: 22CHOL_200POPC_9000SOL_73CAL_146CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 45 mol%), 146 CLA (33 mol%), 73 CAL (17 mol%) and 22 CHOL (cholesterol, 5 mol%) at 310 K. Simulated with Slipids with ECC-scaled ions (Kohagen) in GROMACS 4.6 for 600 ns (55647 atoms). Deposited as NMRlipids Databank simulation 604 and available from https://doi.org/10.5281/zenodo.259354. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 45 mol%), 146 CLA (33 mol%), 73 CAL (17 mol%) and 22 CHOL (cholesterol, 5 mol%) + at 310 K. Simulated with Slipids with ECC-scaled ions (Kohagen) in GROMACS 4.6 + for 600 ns (55647 atoms). Deposited as NMRlipids Databank simulation 604 and available + from https://doi.org/10.5281/zenodo.259354. sameAs: https://doi.org/10.5281/zenodo.259354 datePublished: '2017-01-24' license: @@ -149,7 +155,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.259354 identifier: 10.5281/zenodo.259354 url: https://doi.org/10.5281/zenodo.259354 - name: Popc With Varying Amounts Of Cholesterol, 450 Mm Of Cacl_2. Slipids With Ecc-Scaled Ions + name: Popc With Varying Amounts Of Cholesterol, 450 Mm Of Cacl_2. Slipids With + Ecc-Scaled Ions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/1da/b39/1dab39c51347e2ff353297753f1e8dd86b90b6ef/119b6f2a9b4cd70c4ec19cd2e6d80eaf60dd79ad/README.yaml b/Simulations/1da/b39/1dab39c51347e2ff353297753f1e8dd86b90b6ef/119b6f2a9b4cd70c4ec19cd2e6d80eaf60dd79ad/README.yaml index 01f31ab67e..4abcda0450 100644 --- a/Simulations/1da/b39/1dab39c51347e2ff353297753f1e8dd86b90b6ef/119b6f2a9b4cd70c4ec19cd2e6d80eaf60dd79ad/README.yaml +++ b/Simulations/1da/b39/1dab39c51347e2ff353297753f1e8dd86b90b6ef/119b6f2a9b4cd70c4ec19cd2e6d80eaf60dd79ad/README.yaml @@ -50,9 +50,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 384 bioschema_properties: - name: Molecular dynamics trajectory of a DOPC/CLA/CAL (48:35:17) bilayer at 310 K (Slipids for lipids and Kohagen for ions, GROMACS 4.6, 500 ns) [NMRlipids simulation 384] + name: Molecular dynamics trajectory of a DOPC/CLA/CAL (48:35:17) bilayer at 310 + K (Slipids for lipids and Kohagen for ions, GROMACS 4.6, 500 ns) [NMRlipids simulation + 384] alternateName: 200DOPC_9000SOL_73CAL_146CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, 48 mol%), 146 CLA (35 mol%) and 73 CAL (17 mol%) at 310 K. Simulated with Slipids for lipids and Kohagen for ions in GROMACS 4.6 for 500 ns (54819 atoms). Deposited as NMRlipids Databank simulation 384 and available from https://doi.org/10.5281/zenodo.259443. + description: Molecular dynamics trajectory of a lipid bilayer of 200 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, + 48 mol%), 146 CLA (35 mol%) and 73 CAL (17 mol%) at 310 K. Simulated with Slipids + for lipids and Kohagen for ions in GROMACS 4.6 for 500 ns (54819 atoms). Deposited + as NMRlipids Databank simulation 384 and available from https://doi.org/10.5281/zenodo.259443. sameAs: https://doi.org/10.5281/zenodo.259443 datePublished: '2017-01-24' license: diff --git a/Simulations/1df/fd6/1dffd6d3f52a0cacfae77791cf37d35d185bd06c/beb77c669cf8b12ed759fcc9d60713a74b476bb1/README.yaml b/Simulations/1df/fd6/1dffd6d3f52a0cacfae77791cf37d35d185bd06c/beb77c669cf8b12ed759fcc9d60713a74b476bb1/README.yaml index 11fd9d87a1..bd93ccfed5 100644 --- a/Simulations/1df/fd6/1dffd6d3f52a0cacfae77791cf37d35d185bd06c/beb77c669cf8b12ed759fcc9d60713a74b476bb1/README.yaml +++ b/Simulations/1df/fd6/1dffd6d3f52a0cacfae77791cf37d35d185bd06c/beb77c669cf8b12ed759fcc9d60713a74b476bb1/README.yaml @@ -50,9 +50,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 590 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/CLA/SOD (82:9:9) bilayer at 325 K (CHARMM36, GROMACS 5.0.4, 500 ns) [NMRlipids simulation 590] + name: Molecular dynamics trajectory of a DPPC/CLA/SOD (82:9:9) bilayer at 325 K + (CHARMM36, GROMACS 5.0.4, 500 ns) [NMRlipids simulation 590] alternateName: DPPC_512_NaCl_150mM_325K - description: Molecular dynamics trajectory of a lipid bilayer of 512 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 82 mol%), 55 CLA (9 mol%) and 55 SOD (9 mol%) at 325 K. Simulated with CHARMM36 in GROMACS 5.0.4 for 500 ns (128110 atoms). Deposited as NMRlipids Databank simulation 590 and available from https://doi.org/10.5281/zenodo.1009027. + description: Molecular dynamics trajectory of a lipid bilayer of 512 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 82 mol%), 55 CLA (9 mol%) and 55 SOD (9 mol%) at 325 K. Simulated with CHARMM36 + in GROMACS 5.0.4 for 500 ns (128110 atoms). Deposited as NMRlipids Databank simulation + 590 and available from https://doi.org/10.5281/zenodo.1009027. sameAs: https://doi.org/10.5281/zenodo.1009027 datePublished: '2017-10-11' license: diff --git a/Simulations/1e2/cdc/1e2cdc704d134725e6123404faccf98a7019ff0a/48fd79496a57492cc2d7b7346e3160cae424e7b4/README.yaml b/Simulations/1e2/cdc/1e2cdc704d134725e6123404faccf98a7019ff0a/48fd79496a57492cc2d7b7346e3160cae424e7b4/README.yaml index 0f29de77e0..ee6f1e10fe 100644 --- a/Simulations/1e2/cdc/1e2cdc704d134725e6123404faccf98a7019ff0a/48fd79496a57492cc2d7b7346e3160cae424e7b4/README.yaml +++ b/Simulations/1e2/cdc/1e2cdc704d134725e6123404faccf98a7019ff0a/48fd79496a57492cc2d7b7346e3160cae424e7b4/README.yaml @@ -53,9 +53,13 @@ EXPERIMENT: - 10.1039/C4SM00066H/3 ID: 367 bioschema_properties: - name: Molecular dynamics trajectory of a POPS/SOD (50:50) bilayer at 298 K (CHARMM36-UA, GROMACS, 100 ns) [NMRlipids simulation 367] + name: Molecular dynamics trajectory of a POPS/SOD (50:50) bilayer at 298 K (CHARMM36-UA, + GROMACS, 100 ns) [NMRlipids simulation 367] alternateName: 128POPS_4480SOL_128SOD_298K_v1 - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 50 mol%) and 128 SOD (50 mol%) at 298 K. Simulated with CHARMM36-UA in GROMACS for 100 ns (22144 atoms). Deposited as NMRlipids Databank simulation 367 and available from https://doi.org/10.5281/zenodo.1129458. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, + 50 mol%) and 128 SOD (50 mol%) at 298 K. Simulated with CHARMM36-UA in GROMACS + for 100 ns (22144 atoms). Deposited as NMRlipids Databank simulation 367 and available + from https://doi.org/10.5281/zenodo.1129458. sameAs: https://doi.org/10.5281/zenodo.1129458 datePublished: '2017-12-24' license: diff --git a/Simulations/1e4/319/1e43190ef68526887e7ebb64d8d1770ab91c34c3/ffc63bde73da9d4fdafeeeba2a6e99e786a740b0/README.yaml b/Simulations/1e4/319/1e43190ef68526887e7ebb64d8d1770ab91c34c3/ffc63bde73da9d4fdafeeeba2a6e99e786a740b0/README.yaml index 786e661dfd..41f2a5bb01 100644 --- a/Simulations/1e4/319/1e43190ef68526887e7ebb64d8d1770ab91c34c3/ffc63bde73da9d4fdafeeeba2a6e99e786a740b0/README.yaml +++ b/Simulations/1e4/319/1e43190ef68526887e7ebb64d8d1770ab91c34c3/ffc63bde73da9d4fdafeeeba2a6e99e786a740b0/README.yaml @@ -55,9 +55,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 213 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (84:11:5) bilayer at 310 K (Berger, GROMACS 4.5.5, 100 ns) [NMRlipids simulation 213] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (84:11:5) bilayer at 310 K + (Berger, GROMACS 4.5.5, 100 ns) [NMRlipids simulation 213] alternateName: 128POPC_4452SOL_8CAL_16CLA_310K_Berger - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 84 mol%), 16 CLA (11 mol%) and 8 CAL (5 mol%) at 310 K. Simulated with Berger in GROMACS 4.5.5 for 100 ns (20036 atoms). Deposited as NMRlipids Databank simulation 213 and available from https://doi.org/10.5281/zenodo.887351. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 84 mol%), 16 CLA (11 mol%) and 8 CAL (5 mol%) at 310 K. Simulated with Berger + in GROMACS 4.5.5 for 100 ns (20036 atoms). Deposited as NMRlipids Databank simulation + 213 and available from https://doi.org/10.5281/zenodo.887351. sameAs: https://doi.org/10.5281/zenodo.887351 datePublished: '2017-09-07' license: @@ -148,7 +152,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.887351 identifier: 10.5281/zenodo.887351 url: https://doi.org/10.5281/zenodo.887351 - name: Md Simulation Trajectory Of A Popc Bilayer With 100Mm Cacl2, Berger Force Field For Lipids, Scaled Charges For Ca2+ And Cl- + name: Md Simulation Trajectory Of A Popc Bilayer With 100Mm Cacl2, Berger Force + Field For Lipids, Scaled Charges For Ca2+ And Cl- publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/1e5/44e/1e544ee003324a34db1580597496327540fcc8c4/7a7a0deb18133b57863007662175be761f626971/README.yaml b/Simulations/1e5/44e/1e544ee003324a34db1580597496327540fcc8c4/7a7a0deb18133b57863007662175be761f626971/README.yaml index 9e42d3ce18..31d791d4be 100644 --- a/Simulations/1e5/44e/1e544ee003324a34db1580597496327540fcc8c4/7a7a0deb18133b57863007662175be761f626971/README.yaml +++ b/Simulations/1e5/44e/1e544ee003324a34db1580597496327540fcc8c4/7a7a0deb18133b57863007662175be761f626971/README.yaml @@ -50,9 +50,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 859 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (81:13:6) bilayer at 300 K (CHARMM36, GROMACS 2019.5, 100 ns) [NMRlipids simulation 859] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (81:13:6) bilayer at 300 K + (CHARMM36, GROMACS 2019.5, 100 ns) [NMRlipids simulation 859] alternateName: POPC, 44 w/l, 300 K, 0.1 M CaCl2 - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 81 mol%), 32 CLA (13 mol%) and 16 CAL (6 mol%) at 300 K. Simulated with CHARMM36 in GROMACS 2019.5 for 100 ns (53488 atoms). Deposited as NMRlipids Databank simulation 859 and available from https://doi.org/10.5281/zenodo.6341420. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 81 mol%), 32 CLA (13 mol%) and 16 CAL (6 mol%) at 300 K. Simulated with CHARMM36 + in GROMACS 2019.5 for 100 ns (53488 atoms). Deposited as NMRlipids Databank simulation + 859 and available from https://doi.org/10.5281/zenodo.6341420. sameAs: https://doi.org/10.5281/zenodo.6341420 datePublished: '2022-03-09' license: diff --git a/Simulations/1e7/220/1e722026e02504afa86066116de27b6c94bb59cb/d7891d5e82aff38769f74f28839c94fae8ea5680/README.yaml b/Simulations/1e7/220/1e722026e02504afa86066116de27b6c94bb59cb/d7891d5e82aff38769f74f28839c94fae8ea5680/README.yaml index ff6d902a59..9500dda1da 100644 --- a/Simulations/1e7/220/1e722026e02504afa86066116de27b6c94bb59cb/d7891d5e82aff38769f74f28839c94fae8ea5680/README.yaml +++ b/Simulations/1e7/220/1e722026e02504afa86066116de27b6c94bb59cb/d7891d5e82aff38769f74f28839c94fae8ea5680/README.yaml @@ -50,9 +50,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 481 bioschema_properties: - name: Molecular dynamics trajectory of a DAPC/CHOL (90:10) bilayer at 320 K (CHARMM36, GROMACS, 2000 ns) [NMRlipids simulation 481] + name: Molecular dynamics trajectory of a DAPC/CHOL (90:10) bilayer at 320 K (CHARMM36, + GROMACS, 2000 ns) [NMRlipids simulation 481] alternateName: 260DAPC_28CHOL_11520SOL_320K - description: Molecular dynamics trajectory of a lipid bilayer of 260 DAPC (1,2-diarachidonoyl-sn-glycero-3-phosphocholine, 90 mol%) and 28 CHOL (cholesterol, 10 mol%) at 320 K. Simulated with CHARMM36 in GROMACS for 2000 ns (72512 atoms). Deposited as NMRlipids Databank simulation 481 and available from https://doi.org/10.5281/zenodo.2653735. + description: Molecular dynamics trajectory of a lipid bilayer of 260 DAPC (1,2-diarachidonoyl-sn-glycero-3-phosphocholine, + 90 mol%) and 28 CHOL (cholesterol, 10 mol%) at 320 K. Simulated with CHARMM36 + in GROMACS for 2000 ns (72512 atoms). Deposited as NMRlipids Databank simulation + 481 and available from https://doi.org/10.5281/zenodo.2653735. sameAs: https://doi.org/10.5281/zenodo.2653735 datePublished: '2019-04-29' license: @@ -141,7 +145,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.2653735 identifier: 10.5281/zenodo.2653735 url: https://doi.org/10.5281/zenodo.2653735 - name: Atomistic simulations of DAPC/cholesterol bilayers with one cholesterol restrained to the membrane core + name: Atomistic simulations of DAPC/cholesterol bilayers with one cholesterol + restrained to the membrane core publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/1e8/02f/1e802f341a0d4237aaf224d5c5d85530026be0bf/24e5ed8a70975452504d9092b4f8c51bf5dc6186/README.yaml b/Simulations/1e8/02f/1e802f341a0d4237aaf224d5c5d85530026be0bf/24e5ed8a70975452504d9092b4f8c51bf5dc6186/README.yaml index 5663f0a1cd..f7bcf5de26 100644 --- a/Simulations/1e8/02f/1e802f341a0d4237aaf224d5c5d85530026be0bf/24e5ed8a70975452504d9092b4f8c51bf5dc6186/README.yaml +++ b/Simulations/1e8/02f/1e802f341a0d4237aaf224d5c5d85530026be0bf/24e5ed8a70975452504d9092b4f8c51bf5dc6186/README.yaml @@ -45,9 +45,12 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/1 ID: 675 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 298.15 K (MacRog, GROMACS 2021, 1001 ns) [NMRlipids simulation 675] + name: Molecular dynamics trajectory of a POPC bilayer at 298.15 K (MacRog, GROMACS + 2021, 1001 ns) [NMRlipids simulation 675] alternateName: MacRog_POPC_M - description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 298.15 K. Simulated with MacRog in GROMACS 2021 for 1001 ns (72704 atoms). Deposited as NMRlipids Databank simulation 675 and available from https://doi.org/10.5281/zenodo.7061800. + description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 298.15 K. Simulated with MacRog in GROMACS 2021 for 1001 ns (72704 atoms). + Deposited as NMRlipids Databank simulation 675 and available from https://doi.org/10.5281/zenodo.7061800. sameAs: https://doi.org/10.5281/zenodo.7061800 datePublished: '2022-09-08' license: diff --git a/Simulations/1ed/5f7/1ed5f76310f879efb0cb1c808289db94157f4c9d/2589bd4ed6da50afc223e26a5f214da1aae31e0c/README.yaml b/Simulations/1ed/5f7/1ed5f76310f879efb0cb1c808289db94157f4c9d/2589bd4ed6da50afc223e26a5f214da1aae31e0c/README.yaml index af05d52569..78bcd24f3d 100644 --- a/Simulations/1ed/5f7/1ed5f76310f879efb0cb1c808289db94157f4c9d/2589bd4ed6da50afc223e26a5f214da1aae31e0c/README.yaml +++ b/Simulations/1ed/5f7/1ed5f76310f879efb0cb1c808289db94157f4c9d/2589bd4ed6da50afc223e26a5f214da1aae31e0c/README.yaml @@ -42,9 +42,12 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 381 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 310.15 K (CHARMM36, GROMACS 5.0, 100 ns) [NMRlipids simulation 381] + name: Molecular dynamics trajectory of a POPC bilayer at 310.15 K (CHARMM36, GROMACS + 5.0, 100 ns) [NMRlipids simulation 381] alternateName: 800POPC_36000SOL - description: Molecular dynamics trajectory of a lipid bilayer of 800 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 310.15 K. Simulated with CHARMM36 in GROMACS 5.0 for 100 ns (215200 atoms). Deposited as NMRlipids Databank simulation 381 and available from https://doi.org/10.5281/zenodo.545941. + description: Molecular dynamics trajectory of a lipid bilayer of 800 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 310.15 K. Simulated with CHARMM36 in GROMACS 5.0 for 100 ns (215200 atoms). + Deposited as NMRlipids Databank simulation 381 and available from https://doi.org/10.5281/zenodo.545941. sameAs: https://doi.org/10.5281/zenodo.545941 datePublished: '2017-04-13' license: diff --git a/Simulations/1ef/206/1ef20600128744e801bca89047de22964acd3e9d/edbe8c7309de6bdb695c6fc59615b8c5488ab91b/README.yaml b/Simulations/1ef/206/1ef20600128744e801bca89047de22964acd3e9d/edbe8c7309de6bdb695c6fc59615b8c5488ab91b/README.yaml index ad257d7d8e..13444c350b 100644 --- a/Simulations/1ef/206/1ef20600128744e801bca89047de22964acd3e9d/edbe8c7309de6bdb695c6fc59615b8c5488ab91b/README.yaml +++ b/Simulations/1ef/206/1ef20600128744e801bca89047de22964acd3e9d/edbe8c7309de6bdb695c6fc59615b8c5488ab91b/README.yaml @@ -46,9 +46,12 @@ EXPERIMENT: - 10.1529/biophysj.108.132662/1 ID: 551 bioschema_properties: - name: Molecular dynamics trajectory of a DOPC bilayer at 303.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 551] + name: Molecular dynamics trajectory of a DOPC bilayer at 303.15 K (CHARMM36, GROMACS, + 1001 ns) [NMRlipids simulation 551] alternateName: 256DOPC_12800SOL_303K - description: Molecular dynamics trajectory of a lipid bilayer of 256 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) at 303.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (73728 atoms). Deposited as NMRlipids Databank simulation 551 and available from https://doi.org/10.5281/zenodo.6943086. + description: Molecular dynamics trajectory of a lipid bilayer of 256 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) + at 303.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (73728 atoms). Deposited + as NMRlipids Databank simulation 551 and available from https://doi.org/10.5281/zenodo.6943086. sameAs: https://doi.org/10.5281/zenodo.6943086 datePublished: '2022-07-30' license: diff --git a/Simulations/1f7/166/1f7166e33d5c171678fb15f378425a760bbb612d/da1488d8469d58f547603ed75e699e798458aa83/README.yaml b/Simulations/1f7/166/1f7166e33d5c171678fb15f378425a760bbb612d/da1488d8469d58f547603ed75e699e798458aa83/README.yaml index 5bf08b8fe8..3c3e065dae 100644 --- a/Simulations/1f7/166/1f7166e33d5c171678fb15f378425a760bbb612d/da1488d8469d58f547603ed75e699e798458aa83/README.yaml +++ b/Simulations/1f7/166/1f7166e33d5c171678fb15f378425a760bbb612d/da1488d8469d58f547603ed75e699e798458aa83/README.yaml @@ -55,9 +55,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/9 ID: 166 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (53:47) bilayer at 298.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 166] + name: Molecular dynamics trajectory of a POPC/CHOL (53:47) bilayer at 298.15 K (CHARMM36, + GROMACS, 1001 ns) [NMRlipids simulation 166] alternateName: 256POPC_224CHOL_24000SOL_298K - description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 53 mol%) and 224 CHOL (cholesterol, 47 mol%) at 298.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (122880 atoms). Deposited as NMRlipids Databank simulation 166 and available from https://doi.org/10.5281/zenodo.5767451. + description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 53 mol%) and 224 CHOL (cholesterol, 47 mol%) at 298.15 K. Simulated with CHARMM36 + in GROMACS for 1001 ns (122880 atoms). Deposited as NMRlipids Databank simulation + 166 and available from https://doi.org/10.5281/zenodo.5767451. sameAs: https://doi.org/10.5281/zenodo.5767451 datePublished: '2021-12-08' license: diff --git a/Simulations/1fb/853/1fb853ac78a2c8d0fd5a777b982a8bab73e3a248/6ab24924df5300def6a4ee3fc7accf48b2b40b5a/README.yaml b/Simulations/1fb/853/1fb853ac78a2c8d0fd5a777b982a8bab73e3a248/6ab24924df5300def6a4ee3fc7accf48b2b40b5a/README.yaml index c3f5426049..7c6ef301ec 100644 --- a/Simulations/1fb/853/1fb853ac78a2c8d0fd5a777b982a8bab73e3a248/6ab24924df5300def6a4ee3fc7accf48b2b40b5a/README.yaml +++ b/Simulations/1fb/853/1fb853ac78a2c8d0fd5a777b982a8bab73e3a248/6ab24924df5300def6a4ee3fc7accf48b2b40b5a/README.yaml @@ -48,9 +48,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 133 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (55:30:15) bilayer at 298.15 K (Lipid14 for lipids and AMBER99SB-ILDN for ions, GROMACS 5.0.3, 100 ns) [NMRlipids simulation 133] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (55:30:15) bilayer at 298.15 + K (Lipid14 for lipids and AMBER99SB-ILDN for ions, GROMACS 5.0.3, 100 ns) [NMRlipids + simulation 133] alternateName: 128POPC_6400SOL_35CAL_70CLA_298K - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 55 mol%), 70 CLA (30 mol%) and 35 CAL (15 mol%) at 298.15 K. Simulated with Lipid14 for lipids and AMBER99SB-ILDN for ions in GROMACS 5.0.3 for 100 ns (36457 atoms). Deposited as NMRlipids Databank simulation 133 and available from https://doi.org/10.5281/zenodo.5592698. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 55 mol%), 70 CLA (30 mol%) and 35 CAL (15 mol%) at 298.15 K. Simulated with Lipid14 + for lipids and AMBER99SB-ILDN for ions in GROMACS 5.0.3 for 100 ns (36457 atoms). + Deposited as NMRlipids Databank simulation 133 and available from https://doi.org/10.5281/zenodo.5592698. sameAs: https://doi.org/10.5281/zenodo.5592698 datePublished: '2016-02-18' license: diff --git a/Simulations/207/4f9/2074f96d71ae32a42267bd5407a30ca9b26aca3e/e439d10af0c5ea60c8569780e32b416ea05f24b5/README.yaml b/Simulations/207/4f9/2074f96d71ae32a42267bd5407a30ca9b26aca3e/e439d10af0c5ea60c8569780e32b416ea05f24b5/README.yaml index 16e73560d1..de8f3d7e1b 100644 --- a/Simulations/207/4f9/2074f96d71ae32a42267bd5407a30ca9b26aca3e/e439d10af0c5ea60c8569780e32b416ea05f24b5/README.yaml +++ b/Simulations/207/4f9/2074f96d71ae32a42267bd5407a30ca9b26aca3e/e439d10af0c5ea60c8569780e32b416ea05f24b5/README.yaml @@ -57,9 +57,14 @@ EXPERIMENT: ID: 509 AUTHORS_CONTACT: Kiirikki, M. Anne; Ollila O. H. Samuli bioschema_properties: - name: Molecular dynamics trajectory of a CLA/CAL/POPC/POPG/SOD (53:26:7:7:7) bilayer at 298 K (CHARMM36, GROMACS, 300 ns) [NMRlipids simulation 509] + name: Molecular dynamics trajectory of a CLA/CAL/POPC/POPG/SOD (53:26:7:7:7) bilayer + at 298 K (CHARMM36, GROMACS, 300 ns) [NMRlipids simulation 509] alternateName: POPC:POPG(1:1)+1MCaCl_T298K - description: Molecular dynamics trajectory of a lipid bilayer of 1156 CLA (53 mol%), 578 CAL (26 mol%), 150 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 7 mol%), 150 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 7 mol%) and 150 SOD (7 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for 300 ns (130332 atoms). Deposited as NMRlipids Databank simulation 509 and available from https://doi.org/10.5281/zenodo.3997135. + description: Molecular dynamics trajectory of a lipid bilayer of 1156 CLA (53 mol%), + 578 CAL (26 mol%), 150 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 7 mol%), 150 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 7 mol%) + and 150 SOD (7 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for 300 ns (130332 + atoms). Deposited as NMRlipids Databank simulation 509 and available from https://doi.org/10.5281/zenodo.3997135. sameAs: https://doi.org/10.5281/zenodo.3997135 datePublished: '2020-08-24' license: @@ -149,7 +154,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3997135 identifier: 10.5281/zenodo.3997135 url: https://doi.org/10.5281/zenodo.3997135 - name: POPC:POPG 1:1 MD simulation with CHARMM36 in 1 M CaCL solution and Na+ counter ions + name: POPC:POPG 1:1 MD simulation with CHARMM36 in 1 M CaCL solution and Na+ counter + ions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/207/534/2075347efb80ae66110bc01567d325dbb09a7cd0/7056894a489989f5ec72bc820f82de0130d5c8bf/README.yaml b/Simulations/207/534/2075347efb80ae66110bc01567d325dbb09a7cd0/7056894a489989f5ec72bc820f82de0130d5c8bf/README.yaml index 53061838db..39f6264225 100644 --- a/Simulations/207/534/2075347efb80ae66110bc01567d325dbb09a7cd0/7056894a489989f5ec72bc820f82de0130d5c8bf/README.yaml +++ b/Simulations/207/534/2075347efb80ae66110bc01567d325dbb09a7cd0/7056894a489989f5ec72bc820f82de0130d5c8bf/README.yaml @@ -57,9 +57,13 @@ EXPERIMENT: TLCL_0H: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POT/CLA/TLCL_0H (58:25:9:8) bilayer at 300 K (CHARMM36, GROMACS 5.0.6, 373 ns) [NMRlipids simulation 778] + name: Molecular dynamics trajectory of a POPC/POT/CLA/TLCL_0H (58:25:9:8) bilayer + at 300 K (CHARMM36, GROMACS 5.0.6, 373 ns) [NMRlipids simulation 778] alternateName: TLCL:POPC(20%)50mM-CHARMM - description: Molecular dynamics trajectory of a lipid bilayer of 88 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 58 mol%), 38 POT (25 mol%), 14 CLA (9 mol%) and 12 TLCL_0H (tetralinoleoyl cardiolipin(2−), 8 mol%) at 300 K. Simulated with CHARMM36 in GROMACS 5.0.6 for 373 ns (56826 atoms). Deposited as NMRlipids Databank simulation 778 and available from https://doi.org/10.5281/zenodo.8383558. + description: Molecular dynamics trajectory of a lipid bilayer of 88 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 58 mol%), 38 POT (25 mol%), 14 CLA (9 mol%) and 12 TLCL_0H (tetralinoleoyl cardiolipin(2−), + 8 mol%) at 300 K. Simulated with CHARMM36 in GROMACS 5.0.6 for 373 ns (56826 atoms). + Deposited as NMRlipids Databank simulation 778 and available from https://doi.org/10.5281/zenodo.8383558. sameAs: https://doi.org/10.5281/zenodo.8383558 datePublished: '2023-09-27' license: diff --git a/Simulations/208/241/208241f86895519f5cc67cbea2131b7b265b6ec3/208241f86895519f5cc67cbea2131b7b265b6ec3/README.yaml b/Simulations/208/241/208241f86895519f5cc67cbea2131b7b265b6ec3/208241f86895519f5cc67cbea2131b7b265b6ec3/README.yaml index 55f075756a..b7830b1c85 100644 --- a/Simulations/208/241/208241f86895519f5cc67cbea2131b7b265b6ec3/208241f86895519f5cc67cbea2131b7b265b6ec3/README.yaml +++ b/Simulations/208/241/208241f86895519f5cc67cbea2131b7b265b6ec3/208241f86895519f5cc67cbea2131b7b265b6ec3/README.yaml @@ -45,9 +45,12 @@ EXPERIMENT: FORMFACTOR: - 10.1021/jp511159q/1 bioschema_properties: - name: Molecular dynamics trajectory of a POPE bilayer at 310 K (Charmm-Drude, OPENMM, 360 ns) [NMRlipids simulation 731] + name: Molecular dynamics trajectory of a POPE bilayer at 310 K (Charmm-Drude, OPENMM, + 360 ns) [NMRlipids simulation 731] alternateName: POPE_303K - description: Molecular dynamics trajectory of a lipid bilayer of 144 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) at 310 K. Simulated with Charmm-Drude in OPENMM for 360 ns (51408 atoms). Deposited as NMRlipids Databank simulation 731 and available from https://doi.org/10.5281/zenodo.7602770. + description: Molecular dynamics trajectory of a lipid bilayer of 144 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) + at 310 K. Simulated with Charmm-Drude in OPENMM for 360 ns (51408 atoms). Deposited + as NMRlipids Databank simulation 731 and available from https://doi.org/10.5281/zenodo.7602770. sameAs: https://doi.org/10.5281/zenodo.7602770 datePublished: '2023-02-03' license: @@ -137,7 +140,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.7602770 identifier: 10.5281/zenodo.7602770 url: https://doi.org/10.5281/zenodo.7602770 - name: Pure POPE membrane simulations with the CHARMM-Drude force field at 310K (OpenMM) + name: Pure POPE membrane simulations with the CHARMM-Drude force field at 310K + (OpenMM) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/20c/61b/20c61b1f126cbea496ffdfa84b3532420a0b3088/a57994d2c7ee965bb77455fad03c157702e3dcb2/README.yaml b/Simulations/20c/61b/20c61b1f126cbea496ffdfa84b3532420a0b3088/a57994d2c7ee965bb77455fad03c157702e3dcb2/README.yaml index 792c594e54..86199fb806 100644 --- a/Simulations/20c/61b/20c61b1f126cbea496ffdfa84b3532420a0b3088/a57994d2c7ee965bb77455fad03c157702e3dcb2/README.yaml +++ b/Simulations/20c/61b/20c61b1f126cbea496ffdfa84b3532420a0b3088/a57994d2c7ee965bb77455fad03c157702e3dcb2/README.yaml @@ -42,9 +42,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 676 bioschema_properties: - name: Molecular dynamics trajectory of a DOPC bilayer at 298.15 K (CHARMM36, GROMACS 2021, 1001 ns) [NMRlipids simulation 676] + name: Molecular dynamics trajectory of a DOPC bilayer at 298.15 K (CHARMM36, GROMACS + 2021, 1001 ns) [NMRlipids simulation 676] alternateName: DOPC_S - description: Molecular dynamics trajectory of a lipid bilayer of 64 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) at 298.15 K. Simulated with CHARMM36 in GROMACS 2021 for 1001 ns (18432 atoms). Deposited as NMRlipids Databank simulation 676 and available from https://doi.org/10.5281/zenodo.7103807. + description: Molecular dynamics trajectory of a lipid bilayer of 64 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) + at 298.15 K. Simulated with CHARMM36 in GROMACS 2021 for 1001 ns (18432 atoms). + Deposited as NMRlipids Databank simulation 676 and available from https://doi.org/10.5281/zenodo.7103807. sameAs: https://doi.org/10.5281/zenodo.7103807 datePublished: '2022-09-22' license: diff --git a/Simulations/212/5d4/2125d43a787142402e447de9eb1ebc58b29631f0/7f00c3706565f48caabdf58097ec75329dcbc74c/README.yaml b/Simulations/212/5d4/2125d43a787142402e447de9eb1ebc58b29631f0/7f00c3706565f48caabdf58097ec75329dcbc74c/README.yaml index 876b7f6618..c61ce0ad40 100644 --- a/Simulations/212/5d4/2125d43a787142402e447de9eb1ebc58b29631f0/7f00c3706565f48caabdf58097ec75329dcbc74c/README.yaml +++ b/Simulations/212/5d4/2125d43a787142402e447de9eb1ebc58b29631f0/7f00c3706565f48caabdf58097ec75329dcbc74c/README.yaml @@ -58,9 +58,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 80 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/SOD/CLA/POPS (37:31:24:7) bilayer at 298 K (Lipid17 and Dang ions, GROMACS 2018.0, 1000 ns) [NMRlipids simulation 80] + name: Molecular dynamics trajectory of a POPC/SOD/CLA/POPS (37:31:24:7) bilayer + at 298 K (Lipid17 and Dang ions, GROMACS 2018.0, 1000 ns) [NMRlipids simulation + 80] alternateName: 12POPS_60POPC_3483SOL_51SOD_39CLA_298K - description: Molecular dynamics trajectory of a lipid bilayer of 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 37 mol%), 51 SOD (31 mol%), 39 CLA (24 mol%) and 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 7 mol%) at 298 K. Simulated with Lipid17 and Dang ions in GROMACS 2018.0 for 1000 ns (20103 atoms). Deposited as NMRlipids Databank simulation 80 and available from https://doi.org/10.5281/zenodo.1487895. + description: Molecular dynamics trajectory of a lipid bilayer of 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 37 mol%), 51 SOD (31 mol%), 39 CLA (24 mol%) and 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, + 7 mol%) at 298 K. Simulated with Lipid17 and Dang ions in GROMACS 2018.0 for 1000 + ns (20103 atoms). Deposited as NMRlipids Databank simulation 80 and available + from https://doi.org/10.5281/zenodo.1487895. sameAs: https://doi.org/10.5281/zenodo.1487895 datePublished: '2018-11-14' license: @@ -151,7 +157,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1487895 identifier: 10.5281/zenodo.1487895 url: https://doi.org/10.5281/zenodo.1487895 - name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS with the lipid17 force field, NaCl and KCl salt concentrations + name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS + with the lipid17 force field, NaCl and KCl salt concentrations publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/219/709/219709a1090be0c8ecc1fc3c6362cdf996c1c997/fdf916cac7bed9521a8d6acd71f12207aa12f6fd/README.yaml b/Simulations/219/709/219709a1090be0c8ecc1fc3c6362cdf996c1c997/fdf916cac7bed9521a8d6acd71f12207aa12f6fd/README.yaml index 596851eca7..0912c6dcbf 100644 --- a/Simulations/219/709/219709a1090be0c8ecc1fc3c6362cdf996c1c997/fdf916cac7bed9521a8d6acd71f12207aa12f6fd/README.yaml +++ b/Simulations/219/709/219709a1090be0c8ecc1fc3c6362cdf996c1c997/fdf916cac7bed9521a8d6acd71f12207aa12f6fd/README.yaml @@ -64,9 +64,16 @@ EXPERIMENT: FORMFACTOR: [] ID: 331 bioschema_properties: - name: Molecular dynamics trajectory of a CLA/DMTAP/SOD/DMPC (45:30:15:10) bilayer at 323 K (Berger with DMTAP modification by Gurtovenko et al., GROMACS 3.x, 110 ns) [NMRlipids simulation 331] + name: Molecular dynamics trajectory of a CLA/DMTAP/SOD/DMPC (45:30:15:10) bilayer + at 323 K (Berger with DMTAP modification by Gurtovenko et al., GROMACS 3.x, 110 + ns) [NMRlipids simulation 331] alternateName: 32DMPC_96DMTAP_49SOD_145CLA_5398SOL_323K - description: Molecular dynamics trajectory of a lipid bilayer of 145 CLA (45 mol%), 96 DMTAP (1,2-dimyristoyl-3-trimethylammonium-propane, 30 mol%), 49 SOD (15 mol%) and 32 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine, 10 mol%) at 323 K. Simulated with Berger with DMTAP modification by Gurtovenko et al. in GROMACS 3.x for 110 ns (21604 atoms). Deposited as NMRlipids Databank simulation 331 and available from https://doi.org/10.5281/zenodo.51754. + description: Molecular dynamics trajectory of a lipid bilayer of 145 CLA (45 mol%), + 96 DMTAP (1,2-dimyristoyl-3-trimethylammonium-propane, 30 mol%), 49 SOD (15 mol%) + and 32 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine, 10 mol%) at 323 K. Simulated + with Berger with DMTAP modification by Gurtovenko et al. in GROMACS 3.x for 110 + ns (21604 atoms). Deposited as NMRlipids Databank simulation 331 and available + from https://doi.org/10.5281/zenodo.51754. sameAs: https://doi.org/10.5281/zenodo.51754 datePublished: '2016-05-20' license: @@ -165,7 +172,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.51754 identifier: 10.5281/zenodo.51754 url: https://doi.org/10.5281/zenodo.51754 - name: 'Molecular dynamics simulation trajectory of a cationic lipid bilayer: 75/25 mol% DMTAP/DMPC in 0.5 M NaCl' + name: 'Molecular dynamics simulation trajectory of a cationic lipid bilayer: 75/25 + mol% DMTAP/DMPC in 0.5 M NaCl' publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/21e/025/21e0257dc453a389dfecaf1774e46253c23f4f5d/21e0257dc453a389dfecaf1774e46253c23f4f5d/README.yaml b/Simulations/21e/025/21e0257dc453a389dfecaf1774e46253c23f4f5d/21e0257dc453a389dfecaf1774e46253c23f4f5d/README.yaml index 5809bcdff9..f43ba55bc2 100644 --- a/Simulations/21e/025/21e0257dc453a389dfecaf1774e46253c23f4f5d/21e0257dc453a389dfecaf1774e46253c23f4f5d/README.yaml +++ b/Simulations/21e/025/21e0257dc453a389dfecaf1774e46253c23f4f5d/21e0257dc453a389dfecaf1774e46253c23f4f5d/README.yaml @@ -48,9 +48,14 @@ EXPERIMENT: POPC: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a CLA/POPC/CAL (45:32:23) bilayer at 303 K (Charmm-Drude polarizable2023, OPENMM, 215 ns) [NMRlipids simulation 760] + name: Molecular dynamics trajectory of a CLA/POPC/CAL (45:32:23) bilayer at 303 + K (Charmm-Drude polarizable2023, OPENMM, 215 ns) [NMRlipids simulation 760] alternateName: POPC_790_CaCl2_CHARMMdrude2023_303K - description: Molecular dynamics trajectory of a lipid bilayer of 182 CLA (45 mol%), 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 32 mol%) and 91 CAL (23 mol%) at 303 K. Simulated with Charmm-Drude polarizable2023 in OPENMM for 215 ns (57378 atoms). Deposited as NMRlipids Databank simulation 760 and available from https://doi.org/10.5281/zenodo.7992137. + description: Molecular dynamics trajectory of a lipid bilayer of 182 CLA (45 mol%), + 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 32 mol%) and 91 CAL + (23 mol%) at 303 K. Simulated with Charmm-Drude polarizable2023 in OPENMM for + 215 ns (57378 atoms). Deposited as NMRlipids Databank simulation 760 and available + from https://doi.org/10.5281/zenodo.7992137. sameAs: https://doi.org/10.5281/zenodo.7992137 datePublished: '2023-05-31' license: @@ -133,7 +138,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.7992137 identifier: 10.5281/zenodo.7992137 url: https://doi.org/10.5281/zenodo.7992137 - name: Pure POPC membrane simulations with 790 mM CaCl2 with the CHARMM-Drude2023 force field (OpenMM) + name: Pure POPC membrane simulations with 790 mM CaCl2 with the CHARMM-Drude2023 + force field (OpenMM) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/225/02e/22502e7ac9fc0c6b000bbaf11c853b15aea4da61/71e868c8cfd294df5b3678d9ce7401621825d218/README.yaml b/Simulations/225/02e/22502e7ac9fc0c6b000bbaf11c853b15aea4da61/71e868c8cfd294df5b3678d9ce7401621825d218/README.yaml index cefcff5855..6f6f02d90d 100644 --- a/Simulations/225/02e/22502e7ac9fc0c6b000bbaf11c853b15aea4da61/71e868c8cfd294df5b3678d9ce7401621825d218/README.yaml +++ b/Simulations/225/02e/22502e7ac9fc0c6b000bbaf11c853b15aea4da61/71e868c8cfd294df5b3678d9ce7401621825d218/README.yaml @@ -41,9 +41,12 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 281 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 303 K (CHARMM36, GROMACS 5.0.6, 500 ns) [NMRlipids simulation 281] + name: Molecular dynamics trajectory of a POPC bilayer at 303 K (CHARMM36, GROMACS + 5.0.6, 500 ns) [NMRlipids simulation 281] alternateName: 128POPC_4040SOL_8A-switch_v1 - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 303 K. Simulated with CHARMM36 in GROMACS 5.0.6 for 500 ns (29272 atoms). Deposited as NMRlipids Databank simulation 281 and available from https://doi.org/10.5281/zenodo.164203. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 303 K. Simulated with CHARMM36 in GROMACS 5.0.6 for 500 ns (29272 atoms). Deposited + as NMRlipids Databank simulation 281 and available from https://doi.org/10.5281/zenodo.164203. sameAs: https://doi.org/10.5281/zenodo.164203 datePublished: '2016-11-01' license: diff --git a/Simulations/227/3c2/2273c29e99c9127312973631bf7650a9b6b7f445/9109e7863d6a11a7efd594b86ce12e2c2935e4f9/README.yaml b/Simulations/227/3c2/2273c29e99c9127312973631bf7650a9b6b7f445/9109e7863d6a11a7efd594b86ce12e2c2935e4f9/README.yaml index 4b0c0d48b0..5d66691350 100644 --- a/Simulations/227/3c2/2273c29e99c9127312973631bf7650a9b6b7f445/9109e7863d6a11a7efd594b86ce12e2c2935e4f9/README.yaml +++ b/Simulations/227/3c2/2273c29e99c9127312973631bf7650a9b6b7f445/9109e7863d6a11a7efd594b86ce12e2c2935e4f9/README.yaml @@ -50,9 +50,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/5 ID: 677 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (80:20) bilayer at 298.15 K (MacRog, GROMACS 2021, 1001 ns) [NMRlipids simulation 677] + name: Molecular dynamics trajectory of a POPC/CHOL (80:20) bilayer at 298.15 K (MacRog, + GROMACS 2021, 1001 ns) [NMRlipids simulation 677] alternateName: MacRog_POPC_CHOL20_L - description: Molecular dynamics trajectory of a lipid bilayer of 1024 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 80 mol%) and 256 CHOL (cholesterol, 20 mol%) at 298.15 K. Simulated with MacRog in GROMACS 2021 for 1001 ns (348160 atoms). Deposited as NMRlipids Databank simulation 677 and available from https://doi.org/10.5281/zenodo.7061800. + description: Molecular dynamics trajectory of a lipid bilayer of 1024 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 80 mol%) and 256 CHOL (cholesterol, 20 mol%) at 298.15 K. Simulated with MacRog + in GROMACS 2021 for 1001 ns (348160 atoms). Deposited as NMRlipids Databank simulation + 677 and available from https://doi.org/10.5281/zenodo.7061800. sameAs: https://doi.org/10.5281/zenodo.7061800 datePublished: '2022-09-08' license: diff --git a/Simulations/229/866/2298665351fa0bcf1b3399e4df47eb8832b77eab/85cfc2d0ff1f805b6d989f3f68977b0290fa7399/README.yaml b/Simulations/229/866/2298665351fa0bcf1b3399e4df47eb8832b77eab/85cfc2d0ff1f805b6d989f3f68977b0290fa7399/README.yaml index 1e9bf03768..65bca8b1dd 100644 --- a/Simulations/229/866/2298665351fa0bcf1b3399e4df47eb8832b77eab/85cfc2d0ff1f805b6d989f3f68977b0290fa7399/README.yaml +++ b/Simulations/229/866/2298665351fa0bcf1b3399e4df47eb8832b77eab/85cfc2d0ff1f805b6d989f3f68977b0290fa7399/README.yaml @@ -45,9 +45,12 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/1 ID: 678 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 298.15 K (CHARMM36, GROMACS 2021, 1001 ns) [NMRlipids simulation 678] + name: Molecular dynamics trajectory of a POPC bilayer at 298.15 K (CHARMM36, GROMACS + 2021, 1001 ns) [NMRlipids simulation 678] alternateName: POPC_S - description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 298.15 K. Simulated with CHARMM36 in GROMACS 2021 for 1001 ns (18176 atoms). Deposited as NMRlipids Databank simulation 678 and available from https://doi.org/10.5281/zenodo.7103807. + description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 298.15 K. Simulated with CHARMM36 in GROMACS 2021 for 1001 ns (18176 atoms). + Deposited as NMRlipids Databank simulation 678 and available from https://doi.org/10.5281/zenodo.7103807. sameAs: https://doi.org/10.5281/zenodo.7103807 datePublished: '2022-09-22' license: diff --git a/Simulations/229/866/2298665351fa0bcf1b3399e4df47eb8832b77eab/e74101bfc21ebb8c489d18e1e0b729e2c034fea5/README.yaml b/Simulations/229/866/2298665351fa0bcf1b3399e4df47eb8832b77eab/e74101bfc21ebb8c489d18e1e0b729e2c034fea5/README.yaml index 53c6c56df2..d7282be823 100644 --- a/Simulations/229/866/2298665351fa0bcf1b3399e4df47eb8832b77eab/e74101bfc21ebb8c489d18e1e0b729e2c034fea5/README.yaml +++ b/Simulations/229/866/2298665351fa0bcf1b3399e4df47eb8832b77eab/e74101bfc21ebb8c489d18e1e0b729e2c034fea5/README.yaml @@ -47,9 +47,12 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/1 ID: 546 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 298.15 K (CHARMM36, GROMACS, 471 ns) [NMRlipids simulation 546] + name: Molecular dynamics trajectory of a POPC bilayer at 298.15 K (CHARMM36, GROMACS, + 471 ns) [NMRlipids simulation 546] alternateName: 64POPC_3200SOL_298K - description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 298.15 K. Simulated with CHARMM36 in GROMACS for 471 ns (18176 atoms). Deposited as NMRlipids Databank simulation 546 and available from https://doi.org/10.5281/zenodo.5767451. + description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 298.15 K. Simulated with CHARMM36 in GROMACS for 471 ns (18176 atoms). Deposited + as NMRlipids Databank simulation 546 and available from https://doi.org/10.5281/zenodo.5767451. sameAs: https://doi.org/10.5281/zenodo.5767451 datePublished: '2021-12-08' license: diff --git a/Simulations/22d/7d4/22d7d44243673b42bc622a892ecedf8539083f71/93e7677eaf62f50234a5e9f355f575e7e47b388b/README.yaml b/Simulations/22d/7d4/22d7d44243673b42bc622a892ecedf8539083f71/93e7677eaf62f50234a5e9f355f575e7e47b388b/README.yaml index 496b7423cf..d66f7f1947 100644 --- a/Simulations/22d/7d4/22d7d44243673b42bc622a892ecedf8539083f71/93e7677eaf62f50234a5e9f355f575e7e47b388b/README.yaml +++ b/Simulations/22d/7d4/22d7d44243673b42bc622a892ecedf8539083f71/93e7677eaf62f50234a5e9f355f575e7e47b388b/README.yaml @@ -45,9 +45,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 616 bioschema_properties: - name: Molecular dynamics trajectory of a POPG/SOD (50:50) bilayer at 310 K (Lipid17, GROMACS, 300 ns) [NMRlipids simulation 616] + name: Molecular dynamics trajectory of a POPG/SOD (50:50) bilayer at 310 K (Lipid17, + GROMACS, 300 ns) [NMRlipids simulation 616] alternateName: 500POPG_500SOD_25000SOL_310K - description: Molecular dynamics trajectory of a lipid bilayer of 500 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 50 mol%) and 500 SOD (50 mol%) at 310 K. Simulated with Lipid17 in GROMACS for 300 ns (139000 atoms). Deposited as NMRlipids Databank simulation 616 and available from https://doi.org/10.5281/zenodo.3997214. + description: Molecular dynamics trajectory of a lipid bilayer of 500 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, + 50 mol%) and 500 SOD (50 mol%) at 310 K. Simulated with Lipid17 in GROMACS for + 300 ns (139000 atoms). Deposited as NMRlipids Databank simulation 616 and available + from https://doi.org/10.5281/zenodo.3997214. sameAs: https://doi.org/10.5281/zenodo.3997214 datePublished: '2020-08-24' license: diff --git a/Simulations/22e/bca/22ebcadcf09c64464ff64b5f9b0feaebe15e0729/90beec1e6004b55cd22fac05eb5e1a92148257e9/README.yaml b/Simulations/22e/bca/22ebcadcf09c64464ff64b5f9b0feaebe15e0729/90beec1e6004b55cd22fac05eb5e1a92148257e9/README.yaml index a994340fff..6882b40612 100644 --- a/Simulations/22e/bca/22ebcadcf09c64464ff64b5f9b0feaebe15e0729/90beec1e6004b55cd22fac05eb5e1a92148257e9/README.yaml +++ b/Simulations/22e/bca/22ebcadcf09c64464ff64b5f9b0feaebe15e0729/90beec1e6004b55cd22fac05eb5e1a92148257e9/README.yaml @@ -58,9 +58,15 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 172 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL/CHOL (43:31:16:11) bilayer at 310.15 K (CHARMM36 with incorrect multiplicity in dihedrals and ECC ions, GROMACS 5.0, 800 ns) [NMRlipids simulation 172] + name: Molecular dynamics trajectory of a POPC/CLA/CAL/CHOL (43:31:16:11) bilayer + at 310.15 K (CHARMM36 with incorrect multiplicity in dihedrals and ECC ions, GROMACS + 5.0, 800 ns) [NMRlipids simulation 172] alternateName: 50CHOL_200POPC_9000SOL_73CAL_146CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 43 mol%), 146 CLA (31 mol%), 73 CAL (16 mol%) and 50 CHOL (cholesterol, 11 mol%) at 310.15 K. Simulated with CHARMM36 with incorrect multiplicity in dihedrals and ECC ions in GROMACS 5.0 for 800 ns (57719 atoms). Deposited as NMRlipids Databank simulation 172 and available from https://doi.org/10.5281/zenodo.259376. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 43 mol%), 146 CLA (31 mol%), 73 CAL (16 mol%) and 50 CHOL (cholesterol, 11 mol%) + at 310.15 K. Simulated with CHARMM36 with incorrect multiplicity in dihedrals + and ECC ions in GROMACS 5.0 for 800 ns (57719 atoms). Deposited as NMRlipids Databank + simulation 172 and available from https://doi.org/10.5281/zenodo.259376. sameAs: https://doi.org/10.5281/zenodo.259376 datePublished: '2017-01-24' license: @@ -150,7 +156,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.259376 identifier: 10.5281/zenodo.259376 url: https://doi.org/10.5281/zenodo.259376 - name: Popc With Varying Amounts Of Cholesterol, 450 Mm Of Cacl_2. Charmm36 With Ecc-Scaled Ions + name: Popc With Varying Amounts Of Cholesterol, 450 Mm Of Cacl_2. Charmm36 With + Ecc-Scaled Ions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/232/24d/23224d95390ff0e95967ea1a3d89efb1c6598d6b/4791cafeea88eda925420c35461af89656c4d659/README.yaml b/Simulations/232/24d/23224d95390ff0e95967ea1a3d89efb1c6598d6b/4791cafeea88eda925420c35461af89656c4d659/README.yaml index b0e63f8763..a29189aacb 100644 --- a/Simulations/232/24d/23224d95390ff0e95967ea1a3d89efb1c6598d6b/4791cafeea88eda925420c35461af89656c4d659/README.yaml +++ b/Simulations/232/24d/23224d95390ff0e95967ea1a3d89efb1c6598d6b/4791cafeea88eda925420c35461af89656c4d659/README.yaml @@ -45,9 +45,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 279 bioschema_properties: - name: Molecular dynamics trajectory of a DOPE bilayer at 271 K (Berger-DOPE-2018, GROMACS 4.0.7, 200 ns) [NMRlipids simulation 279] + name: Molecular dynamics trajectory of a DOPE bilayer at 271 K (Berger-DOPE-2018, + GROMACS 4.0.7, 200 ns) [NMRlipids simulation 279] alternateName: 128DOPE_4789SOL_271K_v2 - description: Molecular dynamics trajectory of a lipid bilayer of 128 DOPE (1,2-dioleoyl-sn-glycero-3-phosphoethanolamine) at 271 K. Simulated with Berger-DOPE-2018 in GROMACS 4.0.7 for 200 ns (21279 atoms). Deposited as NMRlipids Databank simulation 279 and available from https://doi.org/10.5281/zenodo.1293905. + description: Molecular dynamics trajectory of a lipid bilayer of 128 DOPE (1,2-dioleoyl-sn-glycero-3-phosphoethanolamine) + at 271 K. Simulated with Berger-DOPE-2018 in GROMACS 4.0.7 for 200 ns (21279 atoms). + Deposited as NMRlipids Databank simulation 279 and available from https://doi.org/10.5281/zenodo.1293905. sameAs: https://doi.org/10.5281/zenodo.1293905 datePublished: '2018-06-20' license: diff --git a/Simulations/233/4de/2334de32d23af1eef39dc59465adbd1b722bfaef/cc01be5dab48618fb091194b3dba2596d485f98d/README.yaml b/Simulations/233/4de/2334de32d23af1eef39dc59465adbd1b722bfaef/cc01be5dab48618fb091194b3dba2596d485f98d/README.yaml index 9ce1a76970..64f276f641 100644 --- a/Simulations/233/4de/2334de32d23af1eef39dc59465adbd1b722bfaef/cc01be5dab48618fb091194b3dba2596d485f98d/README.yaml +++ b/Simulations/233/4de/2334de32d23af1eef39dc59465adbd1b722bfaef/cc01be5dab48618fb091194b3dba2596d485f98d/README.yaml @@ -51,9 +51,13 @@ EXPERIMENT: CHOL: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a DOPC/CHOL (62:38) bilayer at 333.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 642] + name: Molecular dynamics trajectory of a DOPC/CHOL (62:38) bilayer at 333.15 K (CHARMM36, + GROMACS, 1001 ns) [NMRlipids simulation 642] alternateName: 64DOPC_40CHOL_5200SOL_333K - description: Molecular dynamics trajectory of a lipid bilayer of 64 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, 62 mol%) and 40 CHOL (cholesterol, 38 mol%) at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (27392 atoms). Deposited as NMRlipids Databank simulation 642 and available from https://doi.org/10.5281/zenodo.6943929. + description: Molecular dynamics trajectory of a lipid bilayer of 64 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, + 62 mol%) and 40 CHOL (cholesterol, 38 mol%) at 333.15 K. Simulated with CHARMM36 + in GROMACS for 1001 ns (27392 atoms). Deposited as NMRlipids Databank simulation + 642 and available from https://doi.org/10.5281/zenodo.6943929. sameAs: https://doi.org/10.5281/zenodo.6943929 datePublished: '2022-07-30' license: diff --git a/Simulations/235/4e2/2354e21ebaf1a3c1a91bbc39a81bb855a65156a2/5cf395674b97e6840d5f82366b39c1c2910a3e98/README.yaml b/Simulations/235/4e2/2354e21ebaf1a3c1a91bbc39a81bb855a65156a2/5cf395674b97e6840d5f82366b39c1c2910a3e98/README.yaml index d86dad84e0..ad97e2bcac 100644 --- a/Simulations/235/4e2/2354e21ebaf1a3c1a91bbc39a81bb855a65156a2/5cf395674b97e6840d5f82366b39c1c2910a3e98/README.yaml +++ b/Simulations/235/4e2/2354e21ebaf1a3c1a91bbc39a81bb855a65156a2/5cf395674b97e6840d5f82366b39c1c2910a3e98/README.yaml @@ -51,9 +51,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/8 ID: 679 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (62:38) bilayer at 298.15 K (MacRog, GROMACS 2021, 1001 ns) [NMRlipids simulation 679] + name: Molecular dynamics trajectory of a POPC/CHOL (62:38) bilayer at 298.15 K (MacRog, + GROMACS 2021, 1001 ns) [NMRlipids simulation 679] alternateName: MacRog_POPC_CHOL38_M - description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 62 mol%) and 160 CHOL (cholesterol, 38 mol%) at 298.15 K. Simulated with MacRog in GROMACS 2021 for 1001 ns (108544 atoms). Deposited as NMRlipids Databank simulation 679 and available from https://doi.org/10.5281/zenodo.7061800. + description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 62 mol%) and 160 CHOL (cholesterol, 38 mol%) at 298.15 K. Simulated with MacRog + in GROMACS 2021 for 1001 ns (108544 atoms). Deposited as NMRlipids Databank simulation + 679 and available from https://doi.org/10.5281/zenodo.7061800. sameAs: https://doi.org/10.5281/zenodo.7061800 datePublished: '2022-09-08' license: diff --git a/Simulations/243/08b/24308b989eb8ed6c1a7e08943e9e7f89df333e28/2c8e9bbf995f589b3b09ab1ad2da27425acd3a9c/README.yaml b/Simulations/243/08b/24308b989eb8ed6c1a7e08943e9e7f89df333e28/2c8e9bbf995f589b3b09ab1ad2da27425acd3a9c/README.yaml index 1602a5ecec..91d3381ad9 100644 --- a/Simulations/243/08b/24308b989eb8ed6c1a7e08943e9e7f89df333e28/2c8e9bbf995f589b3b09ab1ad2da27425acd3a9c/README.yaml +++ b/Simulations/243/08b/24308b989eb8ed6c1a7e08943e9e7f89df333e28/2c8e9bbf995f589b3b09ab1ad2da27425acd3a9c/README.yaml @@ -55,9 +55,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 296 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (48:35:17) bilayer at 310.15 K (CHARMM36 NBFIX Han, GROMACS, 594 ns) [NMRlipids simulation 296] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (48:35:17) bilayer at 310.15 + K (CHARMM36 NBFIX Han, GROMACS, 594 ns) [NMRlipids simulation 296] alternateName: 200POPC_9000SOL_73CAL_146CLA_310K_NBFIXHan - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 48 mol%), 146 CLA (35 mol%) and 73 CAL (17 mol%) at 310.15 K. Simulated with CHARMM36 NBFIX Han in GROMACS for 594 ns (54019 atoms). Deposited as NMRlipids Databank simulation 296 and available from https://doi.org/10.5281/zenodo.3434396. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 48 mol%), 146 CLA (35 mol%) and 73 CAL (17 mol%) at 310.15 K. Simulated with CHARMM36 + NBFIX Han in GROMACS for 594 ns (54019 atoms). Deposited as NMRlipids Databank + simulation 296 and available from https://doi.org/10.5281/zenodo.3434396. sameAs: https://doi.org/10.5281/zenodo.3434396 datePublished: '2019-09-17' license: diff --git a/Simulations/244/97f/24497f8f740c4466d91660c34cb1c2295265ede5/24497f8f740c4466d91660c34cb1c2295265ede5/README.yaml b/Simulations/244/97f/24497f8f740c4466d91660c34cb1c2295265ede5/24497f8f740c4466d91660c34cb1c2295265ede5/README.yaml index 85551bd0f9..5146ed42ae 100644 --- a/Simulations/244/97f/24497f8f740c4466d91660c34cb1c2295265ede5/24497f8f740c4466d91660c34cb1c2295265ede5/README.yaml +++ b/Simulations/244/97f/24497f8f740c4466d91660c34cb1c2295265ede5/24497f8f740c4466d91660c34cb1c2295265ede5/README.yaml @@ -40,9 +40,12 @@ EXPERIMENT: FORMFACTOR: - 10.1016/j.bbamem.2011.07.022/2 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 303 K (Charmm-Drude polarizable, OPENMM, 200 ns) [NMRlipids simulation 748] + name: Molecular dynamics trajectory of a POPC bilayer at 303 K (Charmm-Drude polarizable, + OPENMM, 200 ns) [NMRlipids simulation 748] alternateName: POPC_CHARMMdrude2023_303K - description: Molecular dynamics trajectory of a lipid bilayer of 72 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 303 K. Simulated with Charmm-Drude polarizable in OPENMM for 200 ns (25163 atoms). Deposited as NMRlipids Databank simulation 748 and available from https://doi.org/10.5281/zenodo.7916287. + description: Molecular dynamics trajectory of a lipid bilayer of 72 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 303 K. Simulated with Charmm-Drude polarizable in OPENMM for 200 ns (25163 + atoms). Deposited as NMRlipids Databank simulation 748 and available from https://doi.org/10.5281/zenodo.7916287. sameAs: https://doi.org/10.5281/zenodo.7916287 datePublished: '2023-05-09' license: @@ -130,7 +133,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.7916287 identifier: 10.5281/zenodo.7916287 url: https://doi.org/10.5281/zenodo.7916287 - name: OpenMM simulations of POPC using the CHARMM Drude2023 force field in xtc format + name: OpenMM simulations of POPC using the CHARMM Drude2023 force field in xtc + format publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/246/c34/246c34ce62d2d5c59c43078c1a25ad6b89751b49/d7be749bbd8cb46ed56d9447055bc6c2f3b49cd9/README.yaml b/Simulations/246/c34/246c34ce62d2d5c59c43078c1a25ad6b89751b49/d7be749bbd8cb46ed56d9447055bc6c2f3b49cd9/README.yaml index 39a550960c..878518d54f 100644 --- a/Simulations/246/c34/246c34ce62d2d5c59c43078c1a25ad6b89751b49/d7be749bbd8cb46ed56d9447055bc6c2f3b49cd9/README.yaml +++ b/Simulations/246/c34/246c34ce62d2d5c59c43078c1a25ad6b89751b49/d7be749bbd8cb46ed56d9447055bc6c2f3b49cd9/README.yaml @@ -49,9 +49,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 423 bioschema_properties: - name: Molecular dynamics trajectory of a SDPE/SDG (91:9) bilayer at 310 K (Lipid17, GROMACS 18.6, 2100 ns) [NMRlipids simulation 423] + name: Molecular dynamics trajectory of a SDPE/SDG (91:9) bilayer at 310 K (Lipid17, + GROMACS 18.6, 2100 ns) [NMRlipids simulation 423] alternateName: 9.4%SDGinSDPEwithLipid17 - description: Molecular dynamics trajectory of a lipid bilayer of 116 SDPE (1-stearoyl-2-docosahexaenoyl-sn-glycero-3-phosphoethanolamine, 91 mol%) and 12 SDG (1-stearoyl-2-docosahexaenoyl-sn-glycerol, 9 mol%) at 310 K. Simulated with Lipid17 in GROMACS 18.6 for 2100 ns (36068 atoms). Deposited as NMRlipids Databank simulation 423 and available from https://doi.org/10.5281/zenodo.6778175. + description: Molecular dynamics trajectory of a lipid bilayer of 116 SDPE (1-stearoyl-2-docosahexaenoyl-sn-glycero-3-phosphoethanolamine, + 91 mol%) and 12 SDG (1-stearoyl-2-docosahexaenoyl-sn-glycerol, 9 mol%) at 310 + K. Simulated with Lipid17 in GROMACS 18.6 for 2100 ns (36068 atoms). Deposited + as NMRlipids Databank simulation 423 and available from https://doi.org/10.5281/zenodo.6778175. sameAs: https://doi.org/10.5281/zenodo.6778175 datePublished: '2022-06-29' license: diff --git a/Simulations/247/965/2479656121ef7f07de1821580d3d9b00c913ca4e/d03acea04b8896f825de65e64bdc9a24b8dd577e/README.yaml b/Simulations/247/965/2479656121ef7f07de1821580d3d9b00c913ca4e/d03acea04b8896f825de65e64bdc9a24b8dd577e/README.yaml index 5ca078433e..ca12ce2341 100644 --- a/Simulations/247/965/2479656121ef7f07de1821580d3d9b00c913ca4e/d03acea04b8896f825de65e64bdc9a24b8dd577e/README.yaml +++ b/Simulations/247/965/2479656121ef7f07de1821580d3d9b00c913ca4e/d03acea04b8896f825de65e64bdc9a24b8dd577e/README.yaml @@ -42,9 +42,12 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 599 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 310 K (CHARMM36, GROMACS 5.0.4, 500 ns) [NMRlipids simulation 599] + name: Molecular dynamics trajectory of a POPC bilayer at 310 K (CHARMM36, GROMACS + 5.0.4, 500 ns) [NMRlipids simulation 599] alternateName: 2512POPC_20480SOL_310K - description: Molecular dynamics trajectory of a lipid bilayer of 512 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 310 K. Simulated with CHARMM36 in GROMACS 5.0.4 for 500 ns (130048 atoms). Deposited as NMRlipids Databank simulation 599 and available from https://doi.org/10.5281/zenodo.1010083. + description: Molecular dynamics trajectory of a lipid bilayer of 512 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 310 K. Simulated with CHARMM36 in GROMACS 5.0.4 for 500 ns (130048 atoms). + Deposited as NMRlipids Databank simulation 599 and available from https://doi.org/10.5281/zenodo.1010083. sameAs: https://doi.org/10.5281/zenodo.1010083 datePublished: '2017-10-12' license: diff --git a/Simulations/247/a95/247a957d4f0e81aabf81b657c8175950427e8ae0/228bdf0773563d9f7b98e46ad9124fa87d0196c9/README.yaml b/Simulations/247/a95/247a957d4f0e81aabf81b657c8175950427e8ae0/228bdf0773563d9f7b98e46ad9124fa87d0196c9/README.yaml index ed9a30c428..312a853ec0 100644 --- a/Simulations/247/a95/247a957d4f0e81aabf81b657c8175950427e8ae0/228bdf0773563d9f7b98e46ad9124fa87d0196c9/README.yaml +++ b/Simulations/247/a95/247a957d4f0e81aabf81b657c8175950427e8ae0/228bdf0773563d9f7b98e46ad9124fa87d0196c9/README.yaml @@ -61,9 +61,15 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 600 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/POPS/SOD/CAL (58:13:12:12:6) bilayer at 320 K (CHARMM36 with NBFIX for calcium ions, GROMACS 2018.6, 434 ns) [NMRlipids simulation 600] + name: Molecular dynamics trajectory of a POPC/CLA/POPS/SOD/CAL (58:13:12:12:6) bilayer + at 320 K (CHARMM36 with NBFIX for calcium ions, GROMACS 2018.6, 434 ns) [NMRlipids + simulation 600] alternateName: 250POPC_50POPS_11190SOL_50SOD_28CAL_56CLA_320K - description: Molecular dynamics trajectory of a lipid bilayer of 250 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 58 mol%), 56 CLA (13 mol%), 50 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 12 mol%), 50 SOD (12 mol%) and 28 CAL (6 mol%) at 320 K. Simulated with CHARMM36 with NBFIX for calcium ions in GROMACS 2018.6 for 434 ns (73554 atoms). Deposited as NMRlipids Databank simulation 600 and available from https://doi.org/10.5281/zenodo.3371327. + description: Molecular dynamics trajectory of a lipid bilayer of 250 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 58 mol%), 56 CLA (13 mol%), 50 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, + 12 mol%), 50 SOD (12 mol%) and 28 CAL (6 mol%) at 320 K. Simulated with CHARMM36 + with NBFIX for calcium ions in GROMACS 2018.6 for 434 ns (73554 atoms). Deposited + as NMRlipids Databank simulation 600 and available from https://doi.org/10.5281/zenodo.3371327. sameAs: https://doi.org/10.5281/zenodo.3371327 datePublished: '2019-08-19' license: diff --git a/Simulations/252/850/252850f5cc664521ef09c0d51c2b35a1110715d8/684fbd9720503cea3b45dc73c6eb05f758cdd0e4/README.yaml b/Simulations/252/850/252850f5cc664521ef09c0d51c2b35a1110715d8/684fbd9720503cea3b45dc73c6eb05f758cdd0e4/README.yaml index 94a978e6ce..22195483fc 100644 --- a/Simulations/252/850/252850f5cc664521ef09c0d51c2b35a1110715d8/684fbd9720503cea3b45dc73c6eb05f758cdd0e4/README.yaml +++ b/Simulations/252/850/252850f5cc664521ef09c0d51c2b35a1110715d8/684fbd9720503cea3b45dc73c6eb05f758cdd0e4/README.yaml @@ -56,9 +56,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 179 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPG/CAL/CLA (39:39:20:1) bilayer at 298 K (CHARMM36, GROMACS, 200 ns) [NMRlipids simulation 179] + name: Molecular dynamics trajectory of a POPC/POPG/CAL/CLA (39:39:20:1) bilayer + at 298 K (CHARMM36, GROMACS, 200 ns) [NMRlipids simulation 179] alternateName: 250POPG_250POPC_128CAL_6CLA_298K_127778Atoms - description: Molecular dynamics trajectory of a lipid bilayer of 250 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 39 mol%), 250 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 39 mol%), 128 CAL (20 mol%) and 6 CLA (1 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for 200 ns (127778 atoms). Deposited as NMRlipids Databank simulation 179 and available from https://doi.org/10.5281/zenodo.3483789. + description: Molecular dynamics trajectory of a lipid bilayer of 250 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 39 mol%), 250 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 39 mol%), + 128 CAL (20 mol%) and 6 CLA (1 mol%) at 298 K. Simulated with CHARMM36 in GROMACS + for 200 ns (127778 atoms). Deposited as NMRlipids Databank simulation 179 and + available from https://doi.org/10.5281/zenodo.3483789. sameAs: https://doi.org/10.5281/zenodo.3483789 datePublished: '2019-10-12' license: diff --git a/Simulations/256/b0c/256b0c2225ce6947b66b5a32c878ab4a46eb4e1a/ac93914e3714a2bb315ba4bf75c9b4b3f9db6607/README.yaml b/Simulations/256/b0c/256b0c2225ce6947b66b5a32c878ab4a46eb4e1a/ac93914e3714a2bb315ba4bf75c9b4b3f9db6607/README.yaml index 7dd8b55a60..72459e4b49 100644 --- a/Simulations/256/b0c/256b0c2225ce6947b66b5a32c878ab4a46eb4e1a/ac93914e3714a2bb315ba4bf75c9b4b3f9db6607/README.yaml +++ b/Simulations/256/b0c/256b0c2225ce6947b66b5a32c878ab4a46eb4e1a/ac93914e3714a2bb315ba4bf75c9b4b3f9db6607/README.yaml @@ -41,9 +41,12 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 224 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 303 K (CHARMM36, GROMACS 5.0.6, 500 ns) [NMRlipids simulation 224] + name: Molecular dynamics trajectory of a POPC bilayer at 303 K (CHARMM36, GROMACS + 5.0.6, 500 ns) [NMRlipids simulation 224] alternateName: 128POPC_4040SOL_8A-switch_v2 - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 303 K. Simulated with CHARMM36 in GROMACS 5.0.6 for 500 ns (29272 atoms). Deposited as NMRlipids Databank simulation 224 and available from https://doi.org/10.5281/zenodo.164203. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 303 K. Simulated with CHARMM36 in GROMACS 5.0.6 for 500 ns (29272 atoms). Deposited + as NMRlipids Databank simulation 224 and available from https://doi.org/10.5281/zenodo.164203. sameAs: https://doi.org/10.5281/zenodo.164203 datePublished: '2016-11-01' license: diff --git a/Simulations/258/5ff/2585ffeb0b723adfe6c465d3cbcf0d0c7bbcb799/0dc596069829892c570ec7fff8bc417d014729e3/README.yaml b/Simulations/258/5ff/2585ffeb0b723adfe6c465d3cbcf0d0c7bbcb799/0dc596069829892c570ec7fff8bc417d014729e3/README.yaml index 4d8b38f8fa..1c5da5e6b8 100644 --- a/Simulations/258/5ff/2585ffeb0b723adfe6c465d3cbcf0d0c7bbcb799/0dc596069829892c570ec7fff8bc417d014729e3/README.yaml +++ b/Simulations/258/5ff/2585ffeb0b723adfe6c465d3cbcf0d0c7bbcb799/0dc596069829892c570ec7fff8bc417d014729e3/README.yaml @@ -52,9 +52,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 131 bioschema_properties: - name: Molecular dynamics trajectory of a DOPC/DOPE (50:50) bilayer at 300 K (Berger (modified to add a repulsive potential onto the ethanolamine hydrogens), GROMACS, 300 ns) [NMRlipids simulation 131] + name: Molecular dynamics trajectory of a DOPC/DOPE (50:50) bilayer at 300 K (Berger + (modified to add a repulsive potential onto the ethanolamine hydrogens), GROMACS, + 300 ns) [NMRlipids simulation 131] alternateName: 128DOPC_128DOPE_11096SOL_300K - description: Molecular dynamics trajectory of a lipid bilayer of 128 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, 50 mol%) and 128 DOPE (1,2-dioleoyl-sn-glycero-3-phosphoethanolamine, 50 mol%) at 300 K. Simulated with Berger (modified to add a repulsive potential onto the ethanolamine hydrogens) in GROMACS for 300 ns (47112 atoms). Deposited as NMRlipids Databank simulation 131 and available from https://doi.org/10.5281/zenodo.1402437. + description: Molecular dynamics trajectory of a lipid bilayer of 128 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, + 50 mol%) and 128 DOPE (1,2-dioleoyl-sn-glycero-3-phosphoethanolamine, 50 mol%) + at 300 K. Simulated with Berger (modified to add a repulsive potential onto the + ethanolamine hydrogens) in GROMACS for 300 ns (47112 atoms). Deposited as NMRlipids + Databank simulation 131 and available from https://doi.org/10.5281/zenodo.1402437. sameAs: https://doi.org/10.5281/zenodo.1402437 datePublished: '2018-08-23' license: @@ -103,7 +109,8 @@ bioschema_properties: inDefinedTermSet: http://edamontology.org url: http://edamontology.org/operation_2476 - Molecular dynamics simulation (gromacs) - - Berger (modified to add a repulsive potential onto the ethanolamine hydrogens) force field + - Berger (modified to add a repulsive potential onto the ethanolamine hydrogens) + force field variableMeasured: - '@type': PropertyValue name: area per lipid diff --git a/Simulations/25a/ce9/25ace931487aad89f9e755125358282fe99d8ea8/7ce1e2a0f5027d28b81cab28c850ef64d5c9aff5/README.yaml b/Simulations/25a/ce9/25ace931487aad89f9e755125358282fe99d8ea8/7ce1e2a0f5027d28b81cab28c850ef64d5c9aff5/README.yaml index 16d2176b68..63cecf0c3c 100644 --- a/Simulations/25a/ce9/25ace931487aad89f9e755125358282fe99d8ea8/7ce1e2a0f5027d28b81cab28c850ef64d5c9aff5/README.yaml +++ b/Simulations/25a/ce9/25ace931487aad89f9e755125358282fe99d8ea8/7ce1e2a0f5027d28b81cab28c850ef64d5c9aff5/README.yaml @@ -46,9 +46,13 @@ TRJ: - - trajSKIP.xtc ID: 317 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPG/SOD (67:17:17) bilayer at 298 K (lipid17, GROMACS, 350 ns) [NMRlipids simulation 317] + name: Molecular dynamics trajectory of a POPC/POPG/SOD (67:17:17) bilayer at 298 + K (lipid17, GROMACS, 350 ns) [NMRlipids simulation 317] alternateName: POPC:POPG(4:1)_T298K - description: Molecular dynamics trajectory of a lipid bilayer of 350 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 67 mol%), 88 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 17 mol%) and 88 SOD (17 mol%) at 298 K. Simulated with lipid17 in GROMACS for 350 ns (136959 atoms). Deposited as NMRlipids Databank simulation 317 and available from https://doi.org/10.5281/zenodo.3693681. + description: Molecular dynamics trajectory of a lipid bilayer of 350 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 67 mol%), 88 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 17 mol%) + and 88 SOD (17 mol%) at 298 K. Simulated with lipid17 in GROMACS for 350 ns (136959 + atoms). Deposited as NMRlipids Databank simulation 317 and available from https://doi.org/10.5281/zenodo.3693681. sameAs: https://doi.org/10.5281/zenodo.3693681 datePublished: '2019-10-23' license: diff --git a/Simulations/25a/fb6/25afb68fd3cf91b95e9a62fb71909d688c5e430c/d6ae10a7d8827f65c7c10330d525deb73feff3d0/README.yaml b/Simulations/25a/fb6/25afb68fd3cf91b95e9a62fb71909d688c5e430c/d6ae10a7d8827f65c7c10330d525deb73feff3d0/README.yaml index cc333d7401..6692a468b8 100644 --- a/Simulations/25a/fb6/25afb68fd3cf91b95e9a62fb71909d688c5e430c/d6ae10a7d8827f65c7c10330d525deb73feff3d0/README.yaml +++ b/Simulations/25a/fb6/25afb68fd3cf91b95e9a62fb71909d688c5e430c/d6ae10a7d8827f65c7c10330d525deb73feff3d0/README.yaml @@ -46,9 +46,12 @@ EXPERIMENT: - 10.1529/biophysj.108.132662/1 ID: 316 bioschema_properties: - name: Molecular dynamics trajectory of a DOPC bilayer at 303.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 316] + name: Molecular dynamics trajectory of a DOPC bilayer at 303.15 K (CHARMM36, GROMACS, + 1001 ns) [NMRlipids simulation 316] alternateName: 64DOPC_3200SOL_303K - description: Molecular dynamics trajectory of a lipid bilayer of 64 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) at 303.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (18432 atoms). Deposited as NMRlipids Databank simulation 316 and available from https://doi.org/10.5281/zenodo.6943086. + description: Molecular dynamics trajectory of a lipid bilayer of 64 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) + at 303.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (18432 atoms). Deposited + as NMRlipids Databank simulation 316 and available from https://doi.org/10.5281/zenodo.6943086. sameAs: https://doi.org/10.5281/zenodo.6943086 datePublished: '2022-07-30' license: diff --git a/Simulations/260/dfc/260dfc4918179de8c74ceee4705136811d6f9b3f/47893dd396b07d5f4f41e12b7d368dab0608385c/README.yaml b/Simulations/260/dfc/260dfc4918179de8c74ceee4705136811d6f9b3f/47893dd396b07d5f4f41e12b7d368dab0608385c/README.yaml index 82f7ae2df1..8cd1d25ced 100644 --- a/Simulations/260/dfc/260dfc4918179de8c74ceee4705136811d6f9b3f/47893dd396b07d5f4f41e12b7d368dab0608385c/README.yaml +++ b/Simulations/260/dfc/260dfc4918179de8c74ceee4705136811d6f9b3f/47893dd396b07d5f4f41e12b7d368dab0608385c/README.yaml @@ -56,9 +56,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 216 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/CLA/SOD/CHOL (74:9:9:9) bilayer at 310 K (Slipids, GROMACS, 1200 ns) [NMRlipids simulation 216] + name: Molecular dynamics trajectory of a DPPC/CLA/SOD/CHOL (74:9:9:9) bilayer at + 310 K (Slipids, GROMACS, 1200 ns) [NMRlipids simulation 216] alternateName: 1032DPPC_120CHOL_46440SOL_124SOD_124CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 1032 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 74 mol%), 124 CLA (9 mol%), 124 SOD (9 mol%) and 120 CHOL (cholesterol, 9 mol%) at 310 K. Simulated with Slipids in GROMACS for 1200 ns (282608 atoms). Deposited as NMRlipids Databank simulation 216 and available from https://doi.org/10.5281/zenodo.3539263. + description: Molecular dynamics trajectory of a lipid bilayer of 1032 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 74 mol%), 124 CLA (9 mol%), 124 SOD (9 mol%) and 120 CHOL (cholesterol, 9 mol%) + at 310 K. Simulated with Slipids in GROMACS for 1200 ns (282608 atoms). Deposited + as NMRlipids Databank simulation 216 and available from https://doi.org/10.5281/zenodo.3539263. sameAs: https://doi.org/10.5281/zenodo.3539263 datePublished: '2019-11-12' license: diff --git a/Simulations/260/dfc/260dfc4918179de8c74ceee4705136811d6f9b3f/605806d980004c78c09f2ac7557c419c46867ccf/README.yaml b/Simulations/260/dfc/260dfc4918179de8c74ceee4705136811d6f9b3f/605806d980004c78c09f2ac7557c419c46867ccf/README.yaml index 02f90cb859..20964f455f 100644 --- a/Simulations/260/dfc/260dfc4918179de8c74ceee4705136811d6f9b3f/605806d980004c78c09f2ac7557c419c46867ccf/README.yaml +++ b/Simulations/260/dfc/260dfc4918179de8c74ceee4705136811d6f9b3f/605806d980004c78c09f2ac7557c419c46867ccf/README.yaml @@ -57,9 +57,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 215 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/CLA/SOD/CHOL (74:9:9:9) bilayer at 310 K (Slipids, GROMACS 4.6, 1400 ns) [NMRlipids simulation 215] + name: Molecular dynamics trajectory of a DPPC/CLA/SOD/CHOL (74:9:9:9) bilayer at + 310 K (Slipids, GROMACS 4.6, 1400 ns) [NMRlipids simulation 215] alternateName: 1032DPPC_120CHOL_46440SOL_124SOD_124CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 1032 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 74 mol%), 124 CLA (9 mol%), 124 SOD (9 mol%) and 120 CHOL (cholesterol, 9 mol%) at 310 K. Simulated with Slipids in GROMACS 4.6 for 1400 ns (282608 atoms). Deposited as NMRlipids Databank simulation 215 and available from https://doi.org/10.5281/zenodo.439066. + description: Molecular dynamics trajectory of a lipid bilayer of 1032 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 74 mol%), 124 CLA (9 mol%), 124 SOD (9 mol%) and 120 CHOL (cholesterol, 9 mol%) + at 310 K. Simulated with Slipids in GROMACS 4.6 for 1400 ns (282608 atoms). Deposited + as NMRlipids Databank simulation 215 and available from https://doi.org/10.5281/zenodo.439066. sameAs: https://doi.org/10.5281/zenodo.439066 datePublished: '2017-03-29' license: @@ -153,7 +157,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.439066 identifier: 10.5281/zenodo.439066 url: https://doi.org/10.5281/zenodo.439066 - name: Simulations Of Dppc/Cholesterol Bilayers With The Slipids Force Field, Part 1/2 + name: Simulations Of Dppc/Cholesterol Bilayers With The Slipids Force Field, Part + 1/2 publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/264/871/2648716fbcde19d1f3815c6a2f10a97554dad3ce/b63dad41a0ec318af07021df97613f5967686bbd/README.yaml b/Simulations/264/871/2648716fbcde19d1f3815c6a2f10a97554dad3ce/b63dad41a0ec318af07021df97613f5967686bbd/README.yaml index 08ef13d3c3..62aa9de8ae 100644 --- a/Simulations/264/871/2648716fbcde19d1f3815c6a2f10a97554dad3ce/b63dad41a0ec318af07021df97613f5967686bbd/README.yaml +++ b/Simulations/264/871/2648716fbcde19d1f3815c6a2f10a97554dad3ce/b63dad41a0ec318af07021df97613f5967686bbd/README.yaml @@ -49,9 +49,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 113 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (90:10) bilayer at 310 K (Slipids, GROMACS 4.6, 500 ns) [NMRlipids simulation 113] + name: Molecular dynamics trajectory of a POPC/CHOL (90:10) bilayer at 310 K (Slipids, + GROMACS 4.6, 500 ns) [NMRlipids simulation 113] alternateName: 200POPC_9000SOL_22CHOL_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 90 mol%) and 22 CHOL (cholesterol, 10 mol%) at 310 K. Simulated with Slipids in GROMACS 4.6 for 500 ns (55428 atoms). Deposited as NMRlipids Databank simulation 113 and available from https://doi.org/10.5281/zenodo.3243328. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 90 mol%) and 22 CHOL (cholesterol, 10 mol%) at 310 K. Simulated with Slipids in + GROMACS 4.6 for 500 ns (55428 atoms). Deposited as NMRlipids Databank simulation + 113 and available from https://doi.org/10.5281/zenodo.3243328. sameAs: https://doi.org/10.5281/zenodo.3243328 datePublished: '2016-08-22' license: @@ -140,7 +144,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3243328 identifier: 10.5281/zenodo.3243328 url: https://doi.org/10.5281/zenodo.3243328 - name: POPC with 0, 10, 20, and 30 mol-% of cholesterol at 310 K. Slipids force field. + name: POPC with 0, 10, 20, and 30 mol-% of cholesterol at 310 K. Slipids force + field. publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/26e/5ce/26e5ce1e41df12e2ce9f6a11be86bfe4813dafd9/991e2ef623ac06747dcbe82cc7f50ec47d1fe48f/README.yaml b/Simulations/26e/5ce/26e5ce1e41df12e2ce9f6a11be86bfe4813dafd9/991e2ef623ac06747dcbe82cc7f50ec47d1fe48f/README.yaml index 9e6eaedebc..2f862f3b36 100644 --- a/Simulations/26e/5ce/26e5ce1e41df12e2ce9f6a11be86bfe4813dafd9/991e2ef623ac06747dcbe82cc7f50ec47d1fe48f/README.yaml +++ b/Simulations/26e/5ce/26e5ce1e41df12e2ce9f6a11be86bfe4813dafd9/991e2ef623ac06747dcbe82cc7f50ec47d1fe48f/README.yaml @@ -49,9 +49,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 700 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (71:29) bilayer at 298.15 K (Lipid17, GROMACS 2021, 1001 ns) [NMRlipids simulation 700] + name: Molecular dynamics trajectory of a POPC/CHOL (71:29) bilayer at 298.15 K (Lipid17, + GROMACS 2021, 1001 ns) [NMRlipids simulation 700] alternateName: Lipid17_POPC_CHOL29_M - description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 71 mol%) and 104 CHOL (cholesterol, 29 mol%) at 298.15 K. Simulated with Lipid17 in GROMACS 2021 for 1001 ns (96000 atoms). Deposited as NMRlipids Databank simulation 700 and available from https://doi.org/10.5281/zenodo.6992065. + description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 71 mol%) and 104 CHOL (cholesterol, 29 mol%) at 298.15 K. Simulated with Lipid17 + in GROMACS 2021 for 1001 ns (96000 atoms). Deposited as NMRlipids Databank simulation + 700 and available from https://doi.org/10.5281/zenodo.6992065. sameAs: https://doi.org/10.5281/zenodo.6992065 datePublished: '2022-08-15' license: diff --git a/Simulations/270/964/270964ae56efe9d02d768327d87a28a723c7c8a7/cb672c0531198ddb85b354a93e62823079f68844/README.yaml b/Simulations/270/964/270964ae56efe9d02d768327d87a28a723c7c8a7/cb672c0531198ddb85b354a93e62823079f68844/README.yaml index b2083bdab3..076b8c6537 100644 --- a/Simulations/270/964/270964ae56efe9d02d768327d87a28a723c7c8a7/cb672c0531198ddb85b354a93e62823079f68844/README.yaml +++ b/Simulations/270/964/270964ae56efe9d02d768327d87a28a723c7c8a7/cb672c0531198ddb85b354a93e62823079f68844/README.yaml @@ -45,9 +45,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 277 bioschema_properties: - name: Molecular dynamics trajectory of a DLPC bilayer at 300 K (Berger-DLPC-13, GROMACS 4.5.4, 80 ns) [NMRlipids simulation 277] + name: Molecular dynamics trajectory of a DLPC bilayer at 300 K (Berger-DLPC-13, + GROMACS 4.5.4, 80 ns) [NMRlipids simulation 277] alternateName: 72DLPC_2016SOL_300K - description: Molecular dynamics trajectory of a lipid bilayer of 72 DLPC (1,2-dilauroyl-sn-glycero-3-phosphocholine) at 300 K. Simulated with Berger-DLPC-13 in GROMACS 4.5.4 for 80 ns (9072 atoms). Deposited as NMRlipids Databank simulation 277 and available from https://doi.org/10.5281/zenodo.16287. + description: Molecular dynamics trajectory of a lipid bilayer of 72 DLPC (1,2-dilauroyl-sn-glycero-3-phosphocholine) + at 300 K. Simulated with Berger-DLPC-13 in GROMACS 4.5.4 for 80 ns (9072 atoms). + Deposited as NMRlipids Databank simulation 277 and available from https://doi.org/10.5281/zenodo.16287. sameAs: https://doi.org/10.5281/zenodo.16287 datePublished: '2015-03-24' license: diff --git a/Simulations/270/9b9/2709b9effcd6928b69fae7d4683a6256d3e82759/2c341c58dcfbaeea6850a7106d8fa1cf9d99aff1/README.yaml b/Simulations/270/9b9/2709b9effcd6928b69fae7d4683a6256d3e82759/2c341c58dcfbaeea6850a7106d8fa1cf9d99aff1/README.yaml index c4a71a2b85..6a64c0f0fd 100644 --- a/Simulations/270/9b9/2709b9effcd6928b69fae7d4683a6256d3e82759/2c341c58dcfbaeea6850a7106d8fa1cf9d99aff1/README.yaml +++ b/Simulations/270/9b9/2709b9effcd6928b69fae7d4683a6256d3e82759/2c341c58dcfbaeea6850a7106d8fa1cf9d99aff1/README.yaml @@ -57,9 +57,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 278 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/DHMDMAB (64:18:18) bilayer at 313 K (ECC-lipids, GROMACS 5.1.4, 200 ns) [NMRlipids simulation 278] + name: Molecular dynamics trajectory of a POPC/CLA/DHMDMAB (64:18:18) bilayer at + 313 K (ECC-lipids, GROMACS 5.1.4, 200 ns) [NMRlipids simulation 278] alternateName: 100POPC_6214SOL_28DHMDMAB_CLA_313K_SPCEmodel - description: Molecular dynamics trajectory of a lipid bilayer of 100 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 64 mol%), 28 CLA (18 mol%) and 28 DHMDMAB (dihexadecyldimethylammonium, 18 mol%) at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 200 ns (35066 atoms). Deposited as NMRlipids Databank simulation 278 and available from https://doi.org/10.5281/zenodo.1118682. + description: Molecular dynamics trajectory of a lipid bilayer of 100 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 64 mol%), 28 CLA (18 mol%) and 28 DHMDMAB (dihexadecyldimethylammonium, 18 mol%) + at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 200 ns (35066 atoms). + Deposited as NMRlipids Databank simulation 278 and available from https://doi.org/10.5281/zenodo.1118682. sameAs: https://doi.org/10.5281/zenodo.1118682 datePublished: '2017-12-19' license: @@ -150,7 +154,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1118682 identifier: 10.5281/zenodo.1118682 url: https://doi.org/10.5281/zenodo.1118682 - name: Simulations Of Popc Lipid Bilayer In Water Solution With Various Molar Fractions Of Cationic Surfactant Dihexadecylammonium Using Ecc-Popc Force Field + name: Simulations Of Popc Lipid Bilayer In Water Solution With Various Molar Fractions + Of Cationic Surfactant Dihexadecylammonium Using Ecc-Popc Force Field publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/271/6a7/2716a7f5db8b194378d8cb69eea9cb2f901836f6/c36a5084a7a5e96b73315c52f3cd5f919c54c91f/README.yaml b/Simulations/271/6a7/2716a7f5db8b194378d8cb69eea9cb2f901836f6/c36a5084a7a5e96b73315c52f3cd5f919c54c91f/README.yaml index 80d5733ccd..fd71edee3b 100644 --- a/Simulations/271/6a7/2716a7f5db8b194378d8cb69eea9cb2f901836f6/c36a5084a7a5e96b73315c52f3cd5f919c54c91f/README.yaml +++ b/Simulations/271/6a7/2716a7f5db8b194378d8cb69eea9cb2f901836f6/c36a5084a7a5e96b73315c52f3cd5f919c54c91f/README.yaml @@ -56,9 +56,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 569 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD/CHOL (35:28:28:9) bilayer at 310 K (Slipids with ions by Smith & Dang, GROMACS 4.6, 200 ns) [NMRlipids simulation 569] + name: Molecular dynamics trajectory of a POPC/CLA/SOD/CHOL (35:28:28:9) bilayer + at 310 K (Slipids with ions by Smith & Dang, GROMACS 4.6, 200 ns) [NMRlipids simulation + 569] alternateName: 50CHOL_200POPC_9000SOL_162SOD_162CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 35 mol%), 162 CLA (28 mol%), 162 SOD (28 mol%) and 50 CHOL (cholesterol, 9 mol%) at 310 K. Simulated with Slipids with ions by Smith & Dang in GROMACS 4.6 for 200 ns (57824 atoms). Deposited as NMRlipids Databank simulation 569 and available from https://doi.org/10.5281/zenodo.259341. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 35 mol%), 162 CLA (28 mol%), 162 SOD (28 mol%) and 50 CHOL (cholesterol, 9 mol%) + at 310 K. Simulated with Slipids with ions by Smith & Dang in GROMACS 4.6 for + 200 ns (57824 atoms). Deposited as NMRlipids Databank simulation 569 and available + from https://doi.org/10.5281/zenodo.259341. sameAs: https://doi.org/10.5281/zenodo.259341 datePublished: '2017-01-24' license: @@ -148,7 +154,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.259341 identifier: 10.5281/zenodo.259341 url: https://doi.org/10.5281/zenodo.259341 - name: Popc With Varying Amounts Of Cholesterol, 1 M Of Nacl. Slipids With Ions By Smith & Dang + name: Popc With Varying Amounts Of Cholesterol, 1 M Of Nacl. Slipids With Ions + By Smith & Dang publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/273/eca/273eca556626ecfe2e8c9dbad5cc8b45cdf2c94b/273eca556626ecfe2e8c9dbad5cc8b45cdf2c94b/README.yaml b/Simulations/273/eca/273eca556626ecfe2e8c9dbad5cc8b45cdf2c94b/273eca556626ecfe2e8c9dbad5cc8b45cdf2c94b/README.yaml index eb788ea6b7..a41c58e158 100644 --- a/Simulations/273/eca/273eca556626ecfe2e8c9dbad5cc8b45cdf2c94b/273eca556626ecfe2e8c9dbad5cc8b45cdf2c94b/README.yaml +++ b/Simulations/273/eca/273eca556626ecfe2e8c9dbad5cc8b45cdf2c94b/273eca556626ecfe2e8c9dbad5cc8b45cdf2c94b/README.yaml @@ -48,9 +48,13 @@ EXPERIMENT: POPC: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (61:20:20) bilayer at 303 K (Charmm-Drude polarizable2023, OPENMM, 224 ns) [NMRlipids simulation 758] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (61:20:20) bilayer at 303 + K (Charmm-Drude polarizable2023, OPENMM, 224 ns) [NMRlipids simulation 758] alternateName: POPC_350_NaCl_CHARMMdrude2023_303K - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 61 mol%), 41 CLA (20 mol%) and 41 SOD (20 mol%) at 303 K. Simulated with Charmm-Drude polarizable2023 in OPENMM for 224 ns (56996 atoms). Deposited as NMRlipids Databank simulation 758 and available from https://doi.org/10.5281/zenodo.8000095. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 61 mol%), 41 CLA (20 mol%) and 41 SOD (20 mol%) at 303 K. Simulated with Charmm-Drude + polarizable2023 in OPENMM for 224 ns (56996 atoms). Deposited as NMRlipids Databank + simulation 758 and available from https://doi.org/10.5281/zenodo.8000095. sameAs: https://doi.org/10.5281/zenodo.8000095 datePublished: '2023-06-02' license: @@ -134,7 +138,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.8000095 identifier: 10.5281/zenodo.8000095 url: https://doi.org/10.5281/zenodo.8000095 - name: Pure POPC membrane simulations with 350 mM NaCl with the CHARMM-Drude2023 force field (OpenMM) + name: Pure POPC membrane simulations with 350 mM NaCl with the CHARMM-Drude2023 + force field (OpenMM) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/287/d83/287d83b5b1cc07c2f7dc5f54a8d74227fc6fc3e2/8cad21af3da1756eeb92edb2ab27873891de645d/README.yaml b/Simulations/287/d83/287d83b5b1cc07c2f7dc5f54a8d74227fc6fc3e2/8cad21af3da1756eeb92edb2ab27873891de645d/README.yaml index 877b9c861b..26412cd255 100644 --- a/Simulations/287/d83/287d83b5b1cc07c2f7dc5f54a8d74227fc6fc3e2/8cad21af3da1756eeb92edb2ab27873891de645d/README.yaml +++ b/Simulations/287/d83/287d83b5b1cc07c2f7dc5f54a8d74227fc6fc3e2/8cad21af3da1756eeb92edb2ab27873891de645d/README.yaml @@ -53,9 +53,13 @@ EXPERIMENT: - 10.1039/C4SM00066H/3 ID: 535 bioschema_properties: - name: Molecular dynamics trajectory of a POPS/SOD (50:50) bilayer at 298 K (GROMOS-CKP, Berger/Chiu NH3 charges and PME, GROMACS, 100 ns) [NMRlipids simulation 535] + name: Molecular dynamics trajectory of a POPS/SOD (50:50) bilayer at 298 K (GROMOS-CKP, + Berger/Chiu NH3 charges and PME, GROMACS, 100 ns) [NMRlipids simulation 535] alternateName: 128POPS_4480SOL_128SOD_298K_GROMOS-CKP_v2 - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 50 mol%) and 128 SOD (50 mol%) at 298 K. Simulated with GROMOS-CKP, Berger/Chiu NH3 charges and PME in GROMACS for 100 ns (20608 atoms). Deposited as NMRlipids Databank simulation 535 and available from https://doi.org/10.5281/zenodo.1129431. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, + 50 mol%) and 128 SOD (50 mol%) at 298 K. Simulated with GROMOS-CKP, Berger/Chiu + NH3 charges and PME in GROMACS for 100 ns (20608 atoms). Deposited as NMRlipids + Databank simulation 535 and available from https://doi.org/10.5281/zenodo.1129431. sameAs: https://doi.org/10.5281/zenodo.1129431 datePublished: '2017-12-24' license: @@ -148,7 +152,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1129431 identifier: 10.5281/zenodo.1129431 url: https://doi.org/10.5281/zenodo.1129431 - name: Gromos-Ckp Pops Simulations (Versions 1 And 2) 298 K With Berger/Chiu Nh3 Charges And Pme + name: Gromos-Ckp Pops Simulations (Versions 1 And 2) 298 K With Berger/Chiu Nh3 + Charges And Pme publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/289/db0/289db0867ffc0e8e7a58ffc7c617f69eb7c60e82/1e1325dc1168c632b9978eaab70e8df6e34afbf3/README.yaml b/Simulations/289/db0/289db0867ffc0e8e7a58ffc7c617f69eb7c60e82/1e1325dc1168c632b9978eaab70e8df6e34afbf3/README.yaml index ad3d78457d..efba61912f 100644 --- a/Simulations/289/db0/289db0867ffc0e8e7a58ffc7c617f69eb7c60e82/1e1325dc1168c632b9978eaab70e8df6e34afbf3/README.yaml +++ b/Simulations/289/db0/289db0867ffc0e8e7a58ffc7c617f69eb7c60e82/1e1325dc1168c632b9978eaab70e8df6e34afbf3/README.yaml @@ -45,9 +45,12 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/1 ID: 701 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 298.15 K (CHARMM36, GROMACS 2021, 1001 ns) [NMRlipids simulation 701] + name: Molecular dynamics trajectory of a POPC bilayer at 298.15 K (CHARMM36, GROMACS + 2021, 1001 ns) [NMRlipids simulation 701] alternateName: POPC_L - description: Molecular dynamics trajectory of a lipid bilayer of 1024 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 298.15 K. Simulated with CHARMM36 in GROMACS 2021 for 1001 ns (290816 atoms). Deposited as NMRlipids Databank simulation 701 and available from https://doi.org/10.5281/zenodo.7103807. + description: Molecular dynamics trajectory of a lipid bilayer of 1024 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 298.15 K. Simulated with CHARMM36 in GROMACS 2021 for 1001 ns (290816 atoms). + Deposited as NMRlipids Databank simulation 701 and available from https://doi.org/10.5281/zenodo.7103807. sameAs: https://doi.org/10.5281/zenodo.7103807 datePublished: '2022-09-22' license: diff --git a/Simulations/294/580/294580f76f29b1bd472b1bfd3ac96bd2c0afc3d8/f9d04d782c95d988832179eb8bf7e78380039dbc/README.yaml b/Simulations/294/580/294580f76f29b1bd472b1bfd3ac96bd2c0afc3d8/f9d04d782c95d988832179eb8bf7e78380039dbc/README.yaml index d023f7d52c..e97418946e 100644 --- a/Simulations/294/580/294580f76f29b1bd472b1bfd3ac96bd2c0afc3d8/f9d04d782c95d988832179eb8bf7e78380039dbc/README.yaml +++ b/Simulations/294/580/294580f76f29b1bd472b1bfd3ac96bd2c0afc3d8/f9d04d782c95d988832179eb8bf7e78380039dbc/README.yaml @@ -51,9 +51,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 415 bioschema_properties: - name: Molecular dynamics trajectory of a CLA/CAL/POPC (59:29:12) bilayer at 313 K (ECC-lipids, GROMACS, 177 ns) [NMRlipids simulation 415] + name: Molecular dynamics trajectory of a CLA/CAL/POPC (59:29:12) bilayer at 313 + K (ECC-lipids, GROMACS, 177 ns) [NMRlipids simulation 415] alternateName: 200POPC_9264SOL_496CAL_992CLA_313K - description: Molecular dynamics trajectory of a lipid bilayer of 992 CLA (59 mol%), 496 CAL (29 mol%) and 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 12 mol%) at 313 K. Simulated with ECC-lipids in GROMACS for 177 ns (56080 atoms). Deposited as NMRlipids Databank simulation 415 and available from https://doi.org/10.5281/zenodo.3434100. + description: Molecular dynamics trajectory of a lipid bilayer of 992 CLA (59 mol%), + 496 CAL (29 mol%) and 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 12 mol%) at 313 K. Simulated with ECC-lipids in GROMACS for 177 ns (56080 atoms). + Deposited as NMRlipids Databank simulation 415 and available from https://doi.org/10.5281/zenodo.3434100. sameAs: https://doi.org/10.5281/zenodo.3434100 datePublished: '2019-09-17' license: diff --git a/Simulations/297/082/2970820884778a46c3362008440cc959f5df09bf/8cdf4d05c8cf012ff685e165ea62836f84153da2/README.yaml b/Simulations/297/082/2970820884778a46c3362008440cc959f5df09bf/8cdf4d05c8cf012ff685e165ea62836f84153da2/README.yaml index 51e8f65eb0..838d5d3cbf 100644 --- a/Simulations/297/082/2970820884778a46c3362008440cc959f5df09bf/8cdf4d05c8cf012ff685e165ea62836f84153da2/README.yaml +++ b/Simulations/297/082/2970820884778a46c3362008440cc959f5df09bf/8cdf4d05c8cf012ff685e165ea62836f84153da2/README.yaml @@ -50,9 +50,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 419 bioschema_properties: - name: Molecular dynamics trajectory of a DAPC/CHOL (90:10) bilayer at 285 K (CHARMM36, GROMACS, 2000 ns) [NMRlipids simulation 419] + name: Molecular dynamics trajectory of a DAPC/CHOL (90:10) bilayer at 285 K (CHARMM36, + GROMACS, 2000 ns) [NMRlipids simulation 419] alternateName: 260DAPC_28CHOL_11520SOL_285K - description: Molecular dynamics trajectory of a lipid bilayer of 260 DAPC (1,2-diarachidonoyl-sn-glycero-3-phosphocholine, 90 mol%) and 28 CHOL (cholesterol, 10 mol%) at 285 K. Simulated with CHARMM36 in GROMACS for 2000 ns (72512 atoms). Deposited as NMRlipids Databank simulation 419 and available from https://doi.org/10.5281/zenodo.2653735. + description: Molecular dynamics trajectory of a lipid bilayer of 260 DAPC (1,2-diarachidonoyl-sn-glycero-3-phosphocholine, + 90 mol%) and 28 CHOL (cholesterol, 10 mol%) at 285 K. Simulated with CHARMM36 + in GROMACS for 2000 ns (72512 atoms). Deposited as NMRlipids Databank simulation + 419 and available from https://doi.org/10.5281/zenodo.2653735. sameAs: https://doi.org/10.5281/zenodo.2653735 datePublished: '2019-04-29' license: @@ -141,7 +145,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.2653735 identifier: 10.5281/zenodo.2653735 url: https://doi.org/10.5281/zenodo.2653735 - name: Atomistic simulations of DAPC/cholesterol bilayers with one cholesterol restrained to the membrane core + name: Atomistic simulations of DAPC/cholesterol bilayers with one cholesterol + restrained to the membrane core publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/299/9ba/2999ba7a8e75cdcbd0493b035d620556aa9a57c5/a92f8b57bb117b56d3bb16edc0d69662e0517d31/README.yaml b/Simulations/299/9ba/2999ba7a8e75cdcbd0493b035d620556aa9a57c5/a92f8b57bb117b56d3bb16edc0d69662e0517d31/README.yaml index e6cea7e51b..e5f282bd3c 100644 --- a/Simulations/299/9ba/2999ba7a8e75cdcbd0493b035d620556aa9a57c5/a92f8b57bb117b56d3bb16edc0d69662e0517d31/README.yaml +++ b/Simulations/299/9ba/2999ba7a8e75cdcbd0493b035d620556aa9a57c5/a92f8b57bb117b56d3bb16edc0d69662e0517d31/README.yaml @@ -41,9 +41,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 386 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 310 K (Lipid17, GROMACS 2018.3, 100 ns) [NMRlipids simulation 386] + name: Molecular dynamics trajectory of a POPC bilayer at 310 K (Lipid17, GROMACS + 2018.3, 100 ns) [NMRlipids simulation 386] alternateName: 500POPC_25000SOL_310K - description: Molecular dynamics trajectory of a lipid bilayer of 500 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 310 K. Simulated with Lipid17 in GROMACS 2018.3 for 100 ns (142000 atoms). Deposited as NMRlipids Databank simulation 386 and available from https://doi.org/10.5281/zenodo.3237657. + description: Molecular dynamics trajectory of a lipid bilayer of 500 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 310 K. Simulated with Lipid17 in GROMACS 2018.3 for 100 ns (142000 atoms). + Deposited as NMRlipids Databank simulation 386 and available from https://doi.org/10.5281/zenodo.3237657. sameAs: https://doi.org/10.5281/zenodo.3237657 datePublished: '2019-06-03' license: diff --git a/Simulations/29c/beb/29cbebd84886bb4d2f8b49e9758abe1fcb617af3/dad189df5c186fe1d522e2c2fa44db7e369f867e/README.yaml b/Simulations/29c/beb/29cbebd84886bb4d2f8b49e9758abe1fcb617af3/dad189df5c186fe1d522e2c2fa44db7e369f867e/README.yaml index aac90101d2..6d1e9a5e77 100644 --- a/Simulations/29c/beb/29cbebd84886bb4d2f8b49e9758abe1fcb617af3/dad189df5c186fe1d522e2c2fa44db7e369f867e/README.yaml +++ b/Simulations/29c/beb/29cbebd84886bb4d2f8b49e9758abe1fcb617af3/dad189df5c186fe1d522e2c2fa44db7e369f867e/README.yaml @@ -67,9 +67,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 95 bioschema_properties: - name: Molecular dynamics trajectory of a CLA/POT/POPC/POPS/SOD (40:40:14:3:3) bilayer at 298 K (ECC-lipids, GROMACS 2018.0, 1000 ns) [NMRlipids simulation 95] + name: Molecular dynamics trajectory of a CLA/POT/POPC/POPS/SOD (40:40:14:3:3) bilayer + at 298 K (ECC-lipids, GROMACS 2018.0, 1000 ns) [NMRlipids simulation 95] alternateName: 12POPS_60POPC_3213SOL_12SOD_174POT_174CLA_298K - description: Molecular dynamics trajectory of a lipid bilayer of 174 CLA (40 mol%), 174 POT (40 mol%), 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 14 mol%), 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 3 mol%) and 12 SOD (3 mol%) at 298 K. Simulated with ECC-lipids in GROMACS 2018.0 for 1000 ns (19563 atoms). Deposited as NMRlipids Databank simulation 95 and available from https://doi.org/10.5281/zenodo.3332778. + description: Molecular dynamics trajectory of a lipid bilayer of 174 CLA (40 mol%), + 174 POT (40 mol%), 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 14 mol%), 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 3 mol%) + and 12 SOD (3 mol%) at 298 K. Simulated with ECC-lipids in GROMACS 2018.0 for + 1000 ns (19563 atoms). Deposited as NMRlipids Databank simulation 95 and available + from https://doi.org/10.5281/zenodo.3332778. sameAs: https://doi.org/10.5281/zenodo.3332778 datePublished: '2018-11-14' license: @@ -162,7 +168,9 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3332778 identifier: 10.5281/zenodo.3332778 url: https://doi.org/10.5281/zenodo.3332778 - name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS (5:1) with ECC-lipids force field, and Na+ (K+) counterions at various additional concentrations of NaCl and KCl + name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS + (5:1) with ECC-lipids force field, and Na+ (K+) counterions at various additional + concentrations of NaCl and KCl publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/2a3/31d/2a331d503b1b832a1d83fc0832b23fea7a30be78/a4bc69848b242679a0a8aea7c3769e7fea922b04/README.yaml b/Simulations/2a3/31d/2a331d503b1b832a1d83fc0832b23fea7a30be78/a4bc69848b242679a0a8aea7c3769e7fea922b04/README.yaml index 3671bc6964..4c6f4b22ce 100644 --- a/Simulations/2a3/31d/2a331d503b1b832a1d83fc0832b23fea7a30be78/a4bc69848b242679a0a8aea7c3769e7fea922b04/README.yaml +++ b/Simulations/2a3/31d/2a331d503b1b832a1d83fc0832b23fea7a30be78/a4bc69848b242679a0a8aea7c3769e7fea922b04/README.yaml @@ -55,9 +55,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 355 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (45:27:27) bilayer at 298.15 K (Ulmschneider, GROMACS 5.0.3, 200 ns) [NMRlipids simulation 355] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (45:27:27) bilayer at 298.15 + K (Ulmschneider, GROMACS 5.0.3, 200 ns) [NMRlipids simulation 355] alternateName: 128POPC_5120SOL_77SOD_77CLA_298K - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 45 mol%), 77 CLA (27 mol%) and 77 SOD (27 mol%) at 298.15 K. Simulated with Ulmschneider in GROMACS 5.0.3 for 200 ns (22170 atoms). Deposited as NMRlipids Databank simulation 355 and available from https://doi.org/10.5281/zenodo.30894. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 45 mol%), 77 CLA (27 mol%) and 77 SOD (27 mol%) at 298.15 K. Simulated with Ulmschneider + in GROMACS 5.0.3 for 200 ns (22170 atoms). Deposited as NMRlipids Databank simulation + 355 and available from https://doi.org/10.5281/zenodo.30894. sameAs: https://doi.org/10.5281/zenodo.30894 datePublished: '2015-09-11' license: diff --git a/Simulations/2a7/755/2a7755b9ad812e97da5c6fd24da051c3ecf11111/0adab61ea57fc14992fce43e417ee66944cac72c/README.yaml b/Simulations/2a7/755/2a7755b9ad812e97da5c6fd24da051c3ecf11111/0adab61ea57fc14992fce43e417ee66944cac72c/README.yaml index 86d063d733..d787df3b3a 100644 --- a/Simulations/2a7/755/2a7755b9ad812e97da5c6fd24da051c3ecf11111/0adab61ea57fc14992fce43e417ee66944cac72c/README.yaml +++ b/Simulations/2a7/755/2a7755b9ad812e97da5c6fd24da051c3ecf11111/0adab61ea57fc14992fce43e417ee66944cac72c/README.yaml @@ -50,9 +50,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 486 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/CLA/SOD (82:9:9) bilayer at 325 K (CHARMM36, GROMACS 5.0.4, 500 ns) [NMRlipids simulation 486] + name: Molecular dynamics trajectory of a DPPC/CLA/SOD (82:9:9) bilayer at 325 K + (CHARMM36, GROMACS 5.0.4, 500 ns) [NMRlipids simulation 486] alternateName: DPPC_512_NaCl_150mM_325K_cutoff09 - description: Molecular dynamics trajectory of a lipid bilayer of 512 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 82 mol%), 55 CLA (9 mol%) and 55 SOD (9 mol%) at 325 K. Simulated with CHARMM36 in GROMACS 5.0.4 for 500 ns (128110 atoms). Deposited as NMRlipids Databank simulation 486 and available from https://doi.org/10.5281/zenodo.1009027. + description: Molecular dynamics trajectory of a lipid bilayer of 512 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 82 mol%), 55 CLA (9 mol%) and 55 SOD (9 mol%) at 325 K. Simulated with CHARMM36 + in GROMACS 5.0.4 for 500 ns (128110 atoms). Deposited as NMRlipids Databank simulation + 486 and available from https://doi.org/10.5281/zenodo.1009027. sameAs: https://doi.org/10.5281/zenodo.1009027 datePublished: '2017-10-11' license: diff --git a/Simulations/2a9/7d1/2a97d1e94052e72834612f60a547347514d3dfbf/c94855d55d49e55b22857b00de9012c190fe5f2e/README.yaml b/Simulations/2a9/7d1/2a97d1e94052e72834612f60a547347514d3dfbf/c94855d55d49e55b22857b00de9012c190fe5f2e/README.yaml index c48bf6fd58..74914f0411 100644 --- a/Simulations/2a9/7d1/2a97d1e94052e72834612f60a547347514d3dfbf/c94855d55d49e55b22857b00de9012c190fe5f2e/README.yaml +++ b/Simulations/2a9/7d1/2a97d1e94052e72834612f60a547347514d3dfbf/c94855d55d49e55b22857b00de9012c190fe5f2e/README.yaml @@ -48,9 +48,12 @@ EXPERIMENT: - 10.1021/jp511159q/1 ID: 233 bioschema_properties: - name: Molecular dynamics trajectory of a POPE bilayer at 310 K (CHARMM36-UA, GROMACS 5.0.6, 100 ns) [NMRlipids simulation 233] + name: Molecular dynamics trajectory of a POPE bilayer at 310 K (CHARMM36-UA, GROMACS + 5.0.6, 100 ns) [NMRlipids simulation 233] alternateName: 336POPE_15254SOL_310K_v1 - description: Molecular dynamics trajectory of a lipid bilayer of 336 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) at 310 K. Simulated with CHARMM36-UA in GROMACS 5.0.6 for 100 ns (67602 atoms). Deposited as NMRlipids Databank simulation 233 and available from https://doi.org/10.5281/zenodo.1293774. + description: Molecular dynamics trajectory of a lipid bilayer of 336 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) + at 310 K. Simulated with CHARMM36-UA in GROMACS 5.0.6 for 100 ns (67602 atoms). + Deposited as NMRlipids Databank simulation 233 and available from https://doi.org/10.5281/zenodo.1293774. sameAs: https://doi.org/10.5281/zenodo.1293774 datePublished: '2018-06-20' license: @@ -140,7 +143,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1293774 identifier: 10.5281/zenodo.1293774 url: https://doi.org/10.5281/zenodo.1293774 - name: 'Charmm36-Ua Pope Simulations (Versions 1 And 2) 310 K (Note: Hexagonal Membrane And Pope Is Called Peua)' + name: 'Charmm36-Ua Pope Simulations (Versions 1 And 2) 310 K (Note: Hexagonal + Membrane And Pope Is Called Peua)' publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/2ac/e9c/2ace9cc5f0b62d5b7f35a1f08ad5184373f9917b/65a08fca74b4d9bbfe2f7a2f8619eab1de8e6e3d/README.yaml b/Simulations/2ac/e9c/2ace9cc5f0b62d5b7f35a1f08ad5184373f9917b/65a08fca74b4d9bbfe2f7a2f8619eab1de8e6e3d/README.yaml index 65db643e51..5e4fc6d304 100644 --- a/Simulations/2ac/e9c/2ace9cc5f0b62d5b7f35a1f08ad5184373f9917b/65a08fca74b4d9bbfe2f7a2f8619eab1de8e6e3d/README.yaml +++ b/Simulations/2ac/e9c/2ace9cc5f0b62d5b7f35a1f08ad5184373f9917b/65a08fca74b4d9bbfe2f7a2f8619eab1de8e6e3d/README.yaml @@ -55,9 +55,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 622 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (44:37:19) bilayer at 313 K (ECC-lipids, GROMACS 5.1.4, 300 ns) [NMRlipids simulation 622] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (44:37:19) bilayer at 313 + K (ECC-lipids, GROMACS 5.1.4, 300 ns) [NMRlipids simulation 622] alternateName: 128POPC_6400SOL_54CAL_108CLA_313K - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 44 mol%), 108 CLA (37 mol%) and 54 CAL (19 mol%) at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 300 ns (36514 atoms). Deposited as NMRlipids Databank simulation 622 and available from https://doi.org/10.5281/zenodo.3335503. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 44 mol%), 108 CLA (37 mol%) and 54 CAL (19 mol%) at 313 K. Simulated with ECC-lipids + in GROMACS 5.1.4 for 300 ns (36514 atoms). Deposited as NMRlipids Databank simulation + 622 and available from https://doi.org/10.5281/zenodo.3335503. sameAs: https://doi.org/10.5281/zenodo.3335503 datePublished: '2017-12-19' license: @@ -149,7 +153,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3335503 identifier: 10.5281/zenodo.3335503 url: https://doi.org/10.5281/zenodo.3335503 - name: Simulations of POPC lipid bilayer in water solution at various NaCl, KCl and CaCl2 concentrations using ECC-POPC force field + name: Simulations of POPC lipid bilayer in water solution at various NaCl, KCl + and CaCl2 concentrations using ECC-POPC force field publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/2b1/62c/2b162c80ec2f03952098021beb74ba2cdd3d16c2/d499d1361ef77c3d931995eefdc3d2dbec565ef0/README.yaml b/Simulations/2b1/62c/2b162c80ec2f03952098021beb74ba2cdd3d16c2/d499d1361ef77c3d931995eefdc3d2dbec565ef0/README.yaml index e2998332fa..8883cfdc6a 100644 --- a/Simulations/2b1/62c/2b162c80ec2f03952098021beb74ba2cdd3d16c2/d499d1361ef77c3d931995eefdc3d2dbec565ef0/README.yaml +++ b/Simulations/2b1/62c/2b162c80ec2f03952098021beb74ba2cdd3d16c2/d499d1361ef77c3d931995eefdc3d2dbec565ef0/README.yaml @@ -48,9 +48,13 @@ EXPERIMENT: - 10.1039/C4SM00066H/3 ID: 502 bioschema_properties: - name: Molecular dynamics trajectory of a POPS/SOD (50:50) bilayer at 298 K (Berger, GROMACS, 100 ns) [NMRlipids simulation 502] + name: Molecular dynamics trajectory of a POPS/SOD (50:50) bilayer at 298 K (Berger, + GROMACS, 100 ns) [NMRlipids simulation 502] alternateName: POPS_298K_Berger - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 50 mol%) and 128 SOD (50 mol%) at 298 K. Simulated with Berger in GROMACS for 100 ns (20608 atoms). Deposited as NMRlipids Databank simulation 502 and available from https://doi.org/10.5281/zenodo.1129425. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, + 50 mol%) and 128 SOD (50 mol%) at 298 K. Simulated with Berger in GROMACS for + 100 ns (20608 atoms). Deposited as NMRlipids Databank simulation 502 and available + from https://doi.org/10.5281/zenodo.1129425. sameAs: https://doi.org/10.5281/zenodo.1129425 datePublished: '2017-12-24' license: diff --git a/Simulations/2b9/b0d/2b9b0d32b79cea2fe66a283bf52e9c1f648393e4/b9251450aa7886b4109908c1ada3d666a77ba77b/README.yaml b/Simulations/2b9/b0d/2b9b0d32b79cea2fe66a283bf52e9c1f648393e4/b9251450aa7886b4109908c1ada3d666a77ba77b/README.yaml index 9e7ea4b8ff..c26d60f6bb 100644 --- a/Simulations/2b9/b0d/2b9b0d32b79cea2fe66a283bf52e9c1f648393e4/b9251450aa7886b4109908c1ada3d666a77ba77b/README.yaml +++ b/Simulations/2b9/b0d/2b9b0d32b79cea2fe66a283bf52e9c1f648393e4/b9251450aa7886b4109908c1ada3d666a77ba77b/README.yaml @@ -47,9 +47,14 @@ DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 429 AUTHORS_CONTACT: Kiirikki, M. Anne; Ollila O. H. Samuli bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPG/SOD (67:17:17) bilayer at 298 K (lipid17ecc, GROMACS, 300 ns) [NMRlipids simulation 429] + name: Molecular dynamics trajectory of a POPC/POPG/SOD (67:17:17) bilayer at 298 + K (lipid17ecc, GROMACS, 300 ns) [NMRlipids simulation 429] alternateName: POPC:POPG(4:1)_T298K - description: Molecular dynamics trajectory of a lipid bilayer of 350 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 67 mol%), 88 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 17 mol%) and 88 SOD (17 mol%) at 298 K. Simulated with lipid17ecc in GROMACS for 300 ns (136959 atoms). Deposited as NMRlipids Databank simulation 429 and available from https://doi.org/10.5281/zenodo.3997154. + description: Molecular dynamics trajectory of a lipid bilayer of 350 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 67 mol%), 88 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 17 mol%) + and 88 SOD (17 mol%) at 298 K. Simulated with lipid17ecc in GROMACS for 300 ns + (136959 atoms). Deposited as NMRlipids Databank simulation 429 and available from + https://doi.org/10.5281/zenodo.3997154. sameAs: https://doi.org/10.5281/zenodo.3997154 datePublished: '2020-08-24' license: diff --git a/Simulations/2bc/3d5/2bc3d554525f409ceb4c66cdb3bb6d20cc76f690/6108561dfaa87c6320d75e06a14b7cd075e3597f/README.yaml b/Simulations/2bc/3d5/2bc3d554525f409ceb4c66cdb3bb6d20cc76f690/6108561dfaa87c6320d75e06a14b7cd075e3597f/README.yaml index fa3ae8fefc..49f1ca25c0 100644 --- a/Simulations/2bc/3d5/2bc3d554525f409ceb4c66cdb3bb6d20cc76f690/6108561dfaa87c6320d75e06a14b7cd075e3597f/README.yaml +++ b/Simulations/2bc/3d5/2bc3d554525f409ceb4c66cdb3bb6d20cc76f690/6108561dfaa87c6320d75e06a14b7cd075e3597f/README.yaml @@ -51,9 +51,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 39 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (84:8:8) bilayer at 298 K (Orange, GROMACS 4.5, 60 ns) [NMRlipids simulation 39] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (84:8:8) bilayer at 298 K + (Orange, GROMACS 4.5, 60 ns) [NMRlipids simulation 39] alternateName: 72POPC_2866SOL_7CLA_7SOD_298K - description: Molecular dynamics trajectory of a lipid bilayer of 72 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 84 mol%), 7 CLA (8 mol%) and 7 SOD (8 mol%) at 298 K. Simulated with Orange in GROMACS 4.5 for 60 ns (12356 atoms). Deposited as NMRlipids Databank simulation 39 and available from https://doi.org/10.5281/zenodo.34491. + description: Molecular dynamics trajectory of a lipid bilayer of 72 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 84 mol%), 7 CLA (8 mol%) and 7 SOD (8 mol%) at 298 K. Simulated with Orange in + GROMACS 4.5 for 60 ns (12356 atoms). Deposited as NMRlipids Databank simulation + 39 and available from https://doi.org/10.5281/zenodo.34491. sameAs: https://doi.org/10.5281/zenodo.34491 datePublished: '2015-12-02' license: @@ -142,7 +146,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.34491 identifier: 10.5281/zenodo.34491 url: https://doi.org/10.5281/zenodo.34491 - name: Md Simulation Trajectory For Popc Bilayer With 140Mm Nacl (Orange, Gromacs 4.5.) + name: Md Simulation Trajectory For Popc Bilayer With 140Mm Nacl (Orange, Gromacs + 4.5.) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/2bf/d08/2bfd08600cb8d901fe9576d6a57b8d107730ae39/2bfd08600cb8d901fe9576d6a57b8d107730ae39/README.yaml b/Simulations/2bf/d08/2bfd08600cb8d901fe9576d6a57b8d107730ae39/2bfd08600cb8d901fe9576d6a57b8d107730ae39/README.yaml index 450d2ea9be..0e0f6c5096 100644 --- a/Simulations/2bf/d08/2bfd08600cb8d901fe9576d6a57b8d107730ae39/2bfd08600cb8d901fe9576d6a57b8d107730ae39/README.yaml +++ b/Simulations/2bf/d08/2bfd08600cb8d901fe9576d6a57b8d107730ae39/2bfd08600cb8d901fe9576d6a57b8d107730ae39/README.yaml @@ -37,9 +37,12 @@ EXPERIMENT: - 10.1021/ja029029o/2 FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a SD5PC bilayer at 303.15 K (CHARMM36m, NAMD 3, 500 ns) [NMRlipids simulation 904] + name: Molecular dynamics trajectory of a SD5PC bilayer at 303.15 K (CHARMM36m, NAMD + 3, 500 ns) [NMRlipids simulation 904] alternateName: SDPC18:0(d35)/22:5n6PC) - description: Molecular dynamics trajectory of a lipid bilayer of 200 SD5PC (1-octadecanoyl-2-(4Z,7Z,10Z,13Z,16Z-docosapentaenoyl)-sn-glycero-3-phosphocholine) at 303.15 K. Simulated with CHARMM36m in NAMD 3 for 500 ns (57600 atoms). Deposited as NMRlipids Databank simulation 904 and available from https://doi.org/10.5281/zenodo.18470730. + description: Molecular dynamics trajectory of a lipid bilayer of 200 SD5PC (1-octadecanoyl-2-(4Z,7Z,10Z,13Z,16Z-docosapentaenoyl)-sn-glycero-3-phosphocholine) + at 303.15 K. Simulated with CHARMM36m in NAMD 3 for 500 ns (57600 atoms). Deposited + as NMRlipids Databank simulation 904 and available from https://doi.org/10.5281/zenodo.18470730. sameAs: https://doi.org/10.5281/zenodo.18470730 datePublished: '2026-02-03' license: @@ -130,7 +133,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.18470730 identifier: 10.5281/zenodo.18470730 url: https://doi.org/10.5281/zenodo.18470730 - name: 1-stearoyl(d35)-2-docosapentaenoyl-sn-glycero-3-phosphocholine (18:0(d35)/22:5n6PC) | SDPC lipid bilayer, 303K, CHARMM36m-WYF forcefield, NAMD 3.0.2, 2* 500 ns + name: 1-stearoyl(d35)-2-docosapentaenoyl-sn-glycero-3-phosphocholine (18:0(d35)/22:5n6PC) + | SDPC lipid bilayer, 303K, CHARMM36m-WYF forcefield, NAMD 3.0.2, 2* 500 ns publisher: Zenodo _source: api: datacite diff --git a/Simulations/2c1/a18/2c1a180e14094b67c31e15f4976e4b3acc648588/b004a96e182a76cc5cb64fce0229208737e7f90e/README.yaml b/Simulations/2c1/a18/2c1a180e14094b67c31e15f4976e4b3acc648588/b004a96e182a76cc5cb64fce0229208737e7f90e/README.yaml index 197f82036a..812db998f1 100644 --- a/Simulations/2c1/a18/2c1a180e14094b67c31e15f4976e4b3acc648588/b004a96e182a76cc5cb64fce0229208737e7f90e/README.yaml +++ b/Simulations/2c1/a18/2c1a180e14094b67c31e15f4976e4b3acc648588/b004a96e182a76cc5cb64fce0229208737e7f90e/README.yaml @@ -45,9 +45,12 @@ EXPERIMENT: - 10.1021/acs.jpcb.4c04719/2 FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 300 K (CHARMM36, GROMACS 2022.4, 290 ns) [NMRlipids simulation 806] + name: Molecular dynamics trajectory of a POPC bilayer at 300 K (CHARMM36, GROMACS + 2022.4, 290 ns) [NMRlipids simulation 806] alternateName: 200POPC_1500SOL_300K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 300 K. Simulated with CHARMM36 in GROMACS 2022.4 for 290 ns (31300 atoms). Deposited as NMRlipids Databank simulation 806 and available from https://doi.org/10.5281/zenodo.10908508. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 300 K. Simulated with CHARMM36 in GROMACS 2022.4 for 290 ns (31300 atoms). + Deposited as NMRlipids Databank simulation 806 and available from https://doi.org/10.5281/zenodo.10908508. sameAs: https://doi.org/10.5281/zenodo.10908508 datePublished: '2024-04-02' license: diff --git a/Simulations/2c6/ae5/2c6ae54d8ce9652f529cd674727a0602d06c8990/2c6ae54d8ce9652f529cd674727a0602d06c8990/README.yaml b/Simulations/2c6/ae5/2c6ae54d8ce9652f529cd674727a0602d06c8990/2c6ae54d8ce9652f529cd674727a0602d06c8990/README.yaml index 179c616504..27b859dfc0 100644 --- a/Simulations/2c6/ae5/2c6ae54d8ce9652f529cd674727a0602d06c8990/2c6ae54d8ce9652f529cd674727a0602d06c8990/README.yaml +++ b/Simulations/2c6/ae5/2c6ae54d8ce9652f529cd674727a0602d06c8990/2c6ae54d8ce9652f529cd674727a0602d06c8990/README.yaml @@ -50,9 +50,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 733 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (61:20:20) bilayer at 303 K (Charmm-Drude polarizable; system has been equilibriated using Charmm36, OPENMM 7.4.1, 514 ns) [NMRlipids simulation 733] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (61:20:20) bilayer at 303 + K (Charmm-Drude polarizable; system has been equilibriated using Charmm36, OPENMM + 7.4.1, 514 ns) [NMRlipids simulation 733] alternateName: 128POPC_6400SOL_41NaCl_303K - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 61 mol%), 41 CLA (20 mol%) and 41 SOD (20 mol%) at 303 K. Simulated with Charmm-Drude polarizable; system has been equilibriated using Charmm36 in OPENMM 7.4.1 for 514 ns (56996 atoms). Deposited as NMRlipids Databank simulation 733 and available from https://doi.org/10.5281/zenodo.7586915. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 61 mol%), 41 CLA (20 mol%) and 41 SOD (20 mol%) at 303 K. Simulated with Charmm-Drude + polarizable; system has been equilibriated using Charmm36 in OPENMM 7.4.1 for + 514 ns (56996 atoms). Deposited as NMRlipids Databank simulation 733 and available + from https://doi.org/10.5281/zenodo.7586915. sameAs: https://doi.org/10.5281/zenodo.7586915 datePublished: '2020-08-19' license: @@ -144,7 +150,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.7586915 identifier: 10.5281/zenodo.7586915 url: https://doi.org/10.5281/zenodo.7586915 - name: Pure POPC Membrane with 350mM NaCl simulations using Drude Polarizable Force Field and OpenMM + name: Pure POPC Membrane with 350mM NaCl simulations using Drude Polarizable Force + Field and OpenMM publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/2c7/f2f/2c7f2fdd10561d0aa4303de786fae6847f253330/709609d15201fb0e1ec21d6992f908474423e70e/README.yaml b/Simulations/2c7/f2f/2c7f2fdd10561d0aa4303de786fae6847f253330/709609d15201fb0e1ec21d6992f908474423e70e/README.yaml index 374c6c0284..164898c8d2 100644 --- a/Simulations/2c7/f2f/2c7f2fdd10561d0aa4303de786fae6847f253330/709609d15201fb0e1ec21d6992f908474423e70e/README.yaml +++ b/Simulations/2c7/f2f/2c7f2fdd10561d0aa4303de786fae6847f253330/709609d15201fb0e1ec21d6992f908474423e70e/README.yaml @@ -40,9 +40,13 @@ EXPERIMENT: C20: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/C20 (86:14) bilayer at 333 K (SLIPIDS, GROMACS, 100 ns) [NMRlipids simulation 897] + name: Molecular dynamics trajectory of a DPPC/C20 (86:14) bilayer at 333 K (SLIPIDS, + GROMACS, 100 ns) [NMRlipids simulation 897] alternateName: DPPC/C20 - description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 86 mol%) and 12 C20 (n-Eicosane, 14 mol%) at 333 K. Simulated with SLIPIDS in GROMACS for 100 ns (13977 atoms). Deposited as NMRlipids Databank simulation 897 and available from https://doi.org/10.5281/zenodo.7572990. + description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 86 mol%) and 12 C20 (n-Eicosane, 14 mol%) at 333 K. Simulated with SLIPIDS in + GROMACS for 100 ns (13977 atoms). Deposited as NMRlipids Databank simulation 897 + and available from https://doi.org/10.5281/zenodo.7572990. sameAs: https://doi.org/10.5281/zenodo.7572990 datePublished: '2023-01-26' license: @@ -134,7 +138,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.7572990 identifier: 10.5281/zenodo.7572990 url: https://doi.org/10.5281/zenodo.7572990 - name: 'MD simulation input files and results for ,,Atomistic MD simulations of n-alkanes in a phospholipid bilayer: CHARMM36 versus Slipids"' + name: 'MD simulation input files and results for ,,Atomistic MD simulations of + n-alkanes in a phospholipid bilayer: CHARMM36 versus Slipids"' publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/2d4/61b/2d461bc9d828af155146162ef42438974e4cbeaf/c8ce4cc36ef6ec7a085cf011176a92d9d746a792/README.yaml b/Simulations/2d4/61b/2d461bc9d828af155146162ef42438974e4cbeaf/c8ce4cc36ef6ec7a085cf011176a92d9d746a792/README.yaml index 369335d1b7..5d77f8c9bc 100644 --- a/Simulations/2d4/61b/2d461bc9d828af155146162ef42438974e4cbeaf/c8ce4cc36ef6ec7a085cf011176a92d9d746a792/README.yaml +++ b/Simulations/2d4/61b/2d461bc9d828af155146162ef42438974e4cbeaf/c8ce4cc36ef6ec7a085cf011176a92d9d746a792/README.yaml @@ -39,9 +39,12 @@ DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 430 AUTHORS_CONTACT: Javanainen, Matti bioschema_properties: - name: Molecular dynamics trajectory of a POPE bilayer at 310 K (CHARMM36, GROMACS, 500 ns) [NMRlipids simulation 430] + name: Molecular dynamics trajectory of a POPE bilayer at 310 K (CHARMM36, GROMACS, + 500 ns) [NMRlipids simulation 430] alternateName: POPE_310K - description: Molecular dynamics trajectory of a lipid bilayer of 144 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) at 310 K. Simulated with CHARMM36 in GROMACS for 500 ns (35280 atoms). Deposited as NMRlipids Databank simulation 430 and available from https://doi.org/10.5281/zenodo.2641987. + description: Molecular dynamics trajectory of a lipid bilayer of 144 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) + at 310 K. Simulated with CHARMM36 in GROMACS for 500 ns (35280 atoms). Deposited + as NMRlipids Databank simulation 430 and available from https://doi.org/10.5281/zenodo.2641987. sameAs: https://doi.org/10.5281/zenodo.2641987 datePublished: '2019-04-16' license: diff --git a/Simulations/2e9/c2b/2e9c2b5fcf3b5504ff9fd97c893d20081f72a5fc/71f038f911d296a0407c424def4d6d6a6c69ea6c/README.yaml b/Simulations/2e9/c2b/2e9c2b5fcf3b5504ff9fd97c893d20081f72a5fc/71f038f911d296a0407c424def4d6d6a6c69ea6c/README.yaml index 43098e5df4..9b7e8223cd 100644 --- a/Simulations/2e9/c2b/2e9c2b5fcf3b5504ff9fd97c893d20081f72a5fc/71f038f911d296a0407c424def4d6d6a6c69ea6c/README.yaml +++ b/Simulations/2e9/c2b/2e9c2b5fcf3b5504ff9fd97c893d20081f72a5fc/71f038f911d296a0407c424def4d6d6a6c69ea6c/README.yaml @@ -43,9 +43,14 @@ SOFTWARE: gromacs DIR_WRK: /usr/home/bort/Databank ID: 248 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 310 K (CHARMM36 (center of mass removed independently for upper leaflet, lower leaflet and water+ions), GROMACS 5.0.4, 500 ns) [NMRlipids simulation 248] + name: Molecular dynamics trajectory of a POPC bilayer at 310 K (CHARMM36 (center + of mass removed independently for upper leaflet, lower leaflet and water+ions), + GROMACS 5.0.4, 500 ns) [NMRlipids simulation 248] alternateName: 72POPC_2880SOL_310K_rmcomm_leaflets - description: Molecular dynamics trajectory of a lipid bilayer of 72 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 310 K. Simulated with CHARMM36 (center of mass removed independently for upper leaflet, lower leaflet and water+ions) in GROMACS 5.0.4 for 500 ns (18288 atoms). Deposited as NMRlipids Databank simulation 248 and available from https://doi.org/10.5281/zenodo.1009607. + description: Molecular dynamics trajectory of a lipid bilayer of 72 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 310 K. Simulated with CHARMM36 (center of mass removed independently for upper + leaflet, lower leaflet and water+ions) in GROMACS 5.0.4 for 500 ns (18288 atoms). + Deposited as NMRlipids Databank simulation 248 and available from https://doi.org/10.5281/zenodo.1009607. sameAs: https://doi.org/10.5281/zenodo.1009607 datePublished: '2017-10-12' license: @@ -98,7 +103,8 @@ bioschema_properties: inDefinedTermSet: http://edamontology.org url: http://edamontology.org/operation_2476 - Molecular dynamics simulation (gromacs 5.0.4) - - CHARMM36 (center of mass removed independently for upper leaflet, lower leaflet and water+ions) force field + - CHARMM36 (center of mass removed independently for upper leaflet, lower leaflet + and water+ions) force field variableMeasured: - '@type': PropertyValue name: area per lipid @@ -138,7 +144,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1009607 identifier: 10.5281/zenodo.1009607 url: https://doi.org/10.5281/zenodo.1009607 - name: Set Simulations Small Pure Bilayers (72 Lipids) Using Charmm36 Ff In Gromacs (Dppc, Popc) + name: Set Simulations Small Pure Bilayers (72 Lipids) Using Charmm36 Ff In Gromacs + (Dppc, Popc) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/2f2/953/2f2953d129ebe9b5086b7ea4bf1a42b2cff273e0/dada612a7104f7a56155224ec5c5f95662feea6b/README.yaml b/Simulations/2f2/953/2f2953d129ebe9b5086b7ea4bf1a42b2cff273e0/dada612a7104f7a56155224ec5c5f95662feea6b/README.yaml index 0ea687a1d0..1420f225de 100644 --- a/Simulations/2f2/953/2f2953d129ebe9b5086b7ea4bf1a42b2cff273e0/dada612a7104f7a56155224ec5c5f95662feea6b/README.yaml +++ b/Simulations/2f2/953/2f2953d129ebe9b5086b7ea4bf1a42b2cff273e0/dada612a7104f7a56155224ec5c5f95662feea6b/README.yaml @@ -46,9 +46,12 @@ EXPERIMENT: - 10.1016/j.bbamem.2011.07.022/10 ID: 309 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC bilayer at 333.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 309] + name: Molecular dynamics trajectory of a DPPC bilayer at 333.15 K (CHARMM36, GROMACS, + 1001 ns) [NMRlipids simulation 309] alternateName: 256DPPC_12800SOL_333K - description: Molecular dynamics trajectory of a lipid bilayer of 256 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (71680 atoms). Deposited as NMRlipids Databank simulation 309 and available from https://doi.org/10.5281/zenodo.6943413. + description: Molecular dynamics trajectory of a lipid bilayer of 256 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) + at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (71680 atoms). Deposited + as NMRlipids Databank simulation 309 and available from https://doi.org/10.5281/zenodo.6943413. sameAs: https://doi.org/10.5281/zenodo.6943413 datePublished: '2022-07-30' license: @@ -139,7 +142,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.6943413 identifier: 10.5281/zenodo.6943413 url: https://doi.org/10.5281/zenodo.6943413 - name: Simulations of different single-component bilayers, three different system sizes + name: Simulations of different single-component bilayers, three different system + sizes publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/2f2/fd1/2f2fd1090599f0d917f14a70eb4ce89c84aa6723/52286e8550f901dd9ecae96198f9e3aa18566755/README.yaml b/Simulations/2f2/fd1/2f2fd1090599f0d917f14a70eb4ce89c84aa6723/52286e8550f901dd9ecae96198f9e3aa18566755/README.yaml index 5246bae6af..a625e8bf2f 100644 --- a/Simulations/2f2/fd1/2f2fd1090599f0d917f14a70eb4ce89c84aa6723/52286e8550f901dd9ecae96198f9e3aa18566755/README.yaml +++ b/Simulations/2f2/fd1/2f2fd1090599f0d917f14a70eb4ce89c84aa6723/52286e8550f901dd9ecae96198f9e3aa18566755/README.yaml @@ -46,9 +46,12 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/1 ID: 814 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 300 K (OPLS4, GROMACS Desmond 2021-3, 500 ns) [NMRlipids simulation 814] + name: Molecular dynamics trajectory of a POPC bilayer at 300 K (OPLS4, GROMACS Desmond + 2021-3, 500 ns) [NMRlipids simulation 814] alternateName: 200POPC_9kSOL_300K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 300 K. Simulated with OPLS4 in GROMACS Desmond 2021-3 for 500 ns (53800 atoms). Deposited as NMRlipids Databank simulation 814 and available from https://doi.org/10.5281/zenodo.10958387. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 300 K. Simulated with OPLS4 in GROMACS Desmond 2021-3 for 500 ns (53800 atoms). + Deposited as NMRlipids Databank simulation 814 and available from https://doi.org/10.5281/zenodo.10958387. sameAs: https://doi.org/10.5281/zenodo.10958387 datePublished: '2024-04-11' license: diff --git a/Simulations/2f6/ef0/2f6ef0068ae0319e0f4b6f860e8d843421b286bd/685f534cf530904ae20f49c0d371b30ea71ff383/README.yaml b/Simulations/2f6/ef0/2f6ef0068ae0319e0f4b6f860e8d843421b286bd/685f534cf530904ae20f49c0d371b30ea71ff383/README.yaml index e182dac56e..435522a598 100644 --- a/Simulations/2f6/ef0/2f6ef0068ae0319e0f4b6f860e8d843421b286bd/685f534cf530904ae20f49c0d371b30ea71ff383/README.yaml +++ b/Simulations/2f6/ef0/2f6ef0068ae0319e0f4b6f860e8d843421b286bd/685f534cf530904ae20f49c0d371b30ea71ff383/README.yaml @@ -50,9 +50,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/5 ID: 702 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (80:20) bilayer at 298.15 K (MacRog, GROMACS 2021, 1001 ns) [NMRlipids simulation 702] + name: Molecular dynamics trajectory of a POPC/CHOL (80:20) bilayer at 298.15 K (MacRog, + GROMACS 2021, 1001 ns) [NMRlipids simulation 702] alternateName: MacRog_POPC_CHOL20_S - description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 80 mol%) and 16 CHOL (cholesterol, 20 mol%) at 298.15 K. Simulated with MacRog in GROMACS 2021 for 1001 ns (21760 atoms). Deposited as NMRlipids Databank simulation 702 and available from https://doi.org/10.5281/zenodo.7061800. + description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 80 mol%) and 16 CHOL (cholesterol, 20 mol%) at 298.15 K. Simulated with MacRog + in GROMACS 2021 for 1001 ns (21760 atoms). Deposited as NMRlipids Databank simulation + 702 and available from https://doi.org/10.5281/zenodo.7061800. sameAs: https://doi.org/10.5281/zenodo.7061800 datePublished: '2022-09-08' license: diff --git a/Simulations/303/d35/303d357a677a09f88481ea36bace99799f87b6af/2f8df1d9506994a2ac02e5177e7650b0ce909a97/README.yaml b/Simulations/303/d35/303d357a677a09f88481ea36bace99799f87b6af/2f8df1d9506994a2ac02e5177e7650b0ce909a97/README.yaml index 6944b2ea1f..b065a5a46c 100644 --- a/Simulations/303/d35/303d357a677a09f88481ea36bace99799f87b6af/2f8df1d9506994a2ac02e5177e7650b0ce909a97/README.yaml +++ b/Simulations/303/d35/303d357a677a09f88481ea36bace99799f87b6af/2f8df1d9506994a2ac02e5177e7650b0ce909a97/README.yaml @@ -50,9 +50,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 193 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/CLA/SOD (82:9:9) bilayer at 325 K (CHARMM36, GROMACS 5.0.4, 499 ns) [NMRlipids simulation 193] + name: Molecular dynamics trajectory of a DPPC/CLA/SOD (82:9:9) bilayer at 325 K + (CHARMM36, GROMACS 5.0.4, 499 ns) [NMRlipids simulation 193] alternateName: DPPC_512_NaCl_150mM_325K_v-rescale - description: Molecular dynamics trajectory of a lipid bilayer of 512 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 82 mol%), 55 CLA (9 mol%) and 55 SOD (9 mol%) at 325 K. Simulated with CHARMM36 in GROMACS 5.0.4 for 499 ns (128110 atoms). Deposited as NMRlipids Databank simulation 193 and available from https://doi.org/10.5281/zenodo.1009027. + description: Molecular dynamics trajectory of a lipid bilayer of 512 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 82 mol%), 55 CLA (9 mol%) and 55 SOD (9 mol%) at 325 K. Simulated with CHARMM36 + in GROMACS 5.0.4 for 499 ns (128110 atoms). Deposited as NMRlipids Databank simulation + 193 and available from https://doi.org/10.5281/zenodo.1009027. sameAs: https://doi.org/10.5281/zenodo.1009027 datePublished: '2017-10-11' license: diff --git a/Simulations/304/765/304765469045020262110ceea29c4a404b503c63/6106499396f3168dd3b1daf338af3a2caaada979/README.yaml b/Simulations/304/765/304765469045020262110ceea29c4a404b503c63/6106499396f3168dd3b1daf338af3a2caaada979/README.yaml index b832834c5a..463e2b86c6 100644 --- a/Simulations/304/765/304765469045020262110ceea29c4a404b503c63/6106499396f3168dd3b1daf338af3a2caaada979/README.yaml +++ b/Simulations/304/765/304765469045020262110ceea29c4a404b503c63/6106499396f3168dd3b1daf338af3a2caaada979/README.yaml @@ -56,9 +56,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 189 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL/CLA/SOD (76:8:8:8) bilayer at 310.15 K (CHARMM36, GROMACS 5.0, 200 ns) [NMRlipids simulation 189] + name: Molecular dynamics trajectory of a POPC/CHOL/CLA/SOD (76:8:8:8) bilayer at + 310.15 K (CHARMM36, GROMACS 5.0, 200 ns) [NMRlipids simulation 189] alternateName: 22CHOL_200POPC_9000SOL_21SOD_21CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 76 mol%), 22 CHOL (cholesterol, 8 mol%), 21 CLA (8 mol%) and 21 SOD (8 mol%) at 310.15 K. Simulated with CHARMM36 in GROMACS 5.0 for 200 ns (55470 atoms). Deposited as NMRlipids Databank simulation 189 and available from https://doi.org/10.5281/zenodo.259392. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 76 mol%), 22 CHOL (cholesterol, 8 mol%), 21 CLA (8 mol%) and 21 SOD (8 mol%) at + 310.15 K. Simulated with CHARMM36 in GROMACS 5.0 for 200 ns (55470 atoms). Deposited + as NMRlipids Databank simulation 189 and available from https://doi.org/10.5281/zenodo.259392. sameAs: https://doi.org/10.5281/zenodo.259392 datePublished: '2017-01-24' license: @@ -148,7 +152,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.259392 identifier: 10.5281/zenodo.259392 url: https://doi.org/10.5281/zenodo.259392 - name: Popc With Varying Amounts Of Cholesterol, 130 Mm Of Nacl. Charmm36 With Default Charmm Ions + name: Popc With Varying Amounts Of Cholesterol, 130 Mm Of Nacl. Charmm36 With + Default Charmm Ions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/304/d91/304d91181da8d43c9fe5eae3f570abf05a76fbcc/3c6d128e6d7cfaaa8b2c87641272a0fba217d21b/README.yaml b/Simulations/304/d91/304d91181da8d43c9fe5eae3f570abf05a76fbcc/3c6d128e6d7cfaaa8b2c87641272a0fba217d21b/README.yaml index 9b5535c06f..7729bbf7c1 100644 --- a/Simulations/304/d91/304d91181da8d43c9fe5eae3f570abf05a76fbcc/3c6d128e6d7cfaaa8b2c87641272a0fba217d21b/README.yaml +++ b/Simulations/304/d91/304d91181da8d43c9fe5eae3f570abf05a76fbcc/3c6d128e6d7cfaaa8b2c87641272a0fba217d21b/README.yaml @@ -44,9 +44,13 @@ EXPERIMENT: SLiPC: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a SLiPC bilayer at 333.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 636] + name: Molecular dynamics trajectory of a SLiPC bilayer at 333.15 K (CHARMM36, GROMACS, + 1001 ns) [NMRlipids simulation 636] alternateName: 1024SLiPC_51200SOL_333K - description: Molecular dynamics trajectory of a lipid bilayer of 1024 SLiPC (1-(18:0)-2-(18:2 $^{\Delta9,12}$)-sn-glycero-3-phosphocholine) at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (294912 atoms). Deposited as NMRlipids Databank simulation 636 and available from https://doi.org/10.5281/zenodo.6943413. + description: Molecular dynamics trajectory of a lipid bilayer of 1024 SLiPC (1-(18:0)-2-(18:2 + $^{\Delta9,12}$)-sn-glycero-3-phosphocholine) at 333.15 K. Simulated with CHARMM36 + in GROMACS for 1001 ns (294912 atoms). Deposited as NMRlipids Databank simulation + 636 and available from https://doi.org/10.5281/zenodo.6943413. sameAs: https://doi.org/10.5281/zenodo.6943413 datePublished: '2022-07-30' license: @@ -134,7 +138,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.6943413 identifier: 10.5281/zenodo.6943413 url: https://doi.org/10.5281/zenodo.6943413 - name: Simulations of different single-component bilayers, three different system sizes + name: Simulations of different single-component bilayers, three different system + sizes publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/306/0e0/3060e0da10ae3325d69b59feef3a2249b299a706/9789f36a4d076909e29a14c8cc702b794e358691/README.yaml b/Simulations/306/0e0/3060e0da10ae3325d69b59feef3a2249b299a706/9789f36a4d076909e29a14c8cc702b794e358691/README.yaml index 0e8c552493..aec7275f42 100644 --- a/Simulations/306/0e0/3060e0da10ae3325d69b59feef3a2249b299a706/9789f36a4d076909e29a14c8cc702b794e358691/README.yaml +++ b/Simulations/306/0e0/3060e0da10ae3325d69b59feef3a2249b299a706/9789f36a4d076909e29a14c8cc702b794e358691/README.yaml @@ -56,9 +56,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 458 bioschema_properties: - name: Molecular dynamics trajectory of a POPE/SOD/POPG/CLA (52:24:17:7) bilayer at 310 K (Lipid17 for lipids and AMBER ff15ipq for ions, GROMACS 5.1.2, 100 ns) [NMRlipids simulation 458] + name: Molecular dynamics trajectory of a POPE/SOD/POPG/CLA (52:24:17:7) bilayer + at 310 K (Lipid17 for lipids and AMBER ff15ipq for ions, GROMACS 5.1.2, 100 ns) + [NMRlipids simulation 458] alternateName: 371POPE_126POPG_176SOD_50CLA_25000SOL_310K - description: Molecular dynamics trajectory of a lipid bilayer of 374 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 52 mol%), 176 SOD (24 mol%), 126 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 17 mol%) and 50 CLA (7 mol%) at 310 K. Simulated with Lipid17 for lipids and AMBER ff15ipq for ions in GROMACS 5.1.2 for 100 ns (137978 atoms). Deposited as NMRlipids Databank simulation 458 and available from https://doi.org/10.5281/zenodo.2579061. + description: Molecular dynamics trajectory of a lipid bilayer of 374 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, + 52 mol%), 176 SOD (24 mol%), 126 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, + 17 mol%) and 50 CLA (7 mol%) at 310 K. Simulated with Lipid17 for lipids and AMBER + ff15ipq for ions in GROMACS 5.1.2 for 100 ns (137978 atoms). Deposited as NMRlipids + Databank simulation 458 and available from https://doi.org/10.5281/zenodo.2579061. sameAs: https://doi.org/10.5281/zenodo.2579061 datePublished: '2019-02-27' license: @@ -151,7 +157,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.2579061 identifier: 10.5281/zenodo.2579061 url: https://doi.org/10.5281/zenodo.2579061 - name: LIPID17 POPG-POPE 1:3 Bilayer Simulation (Last 100 ns, 150 mM NaCl, 310 K ) + name: LIPID17 POPG-POPE 1:3 Bilayer Simulation (Last 100 ns, 150 mM NaCl, 310 + K ) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/30e/6ee/30e6eedb46c2d313b709697ae73f0671c5079dc6/7aac3f64c8467f18f5265bc5aa63ed6895c348cf/README.yaml b/Simulations/30e/6ee/30e6eedb46c2d313b709697ae73f0671c5079dc6/7aac3f64c8467f18f5265bc5aa63ed6895c348cf/README.yaml index 9d47665838..e22ecfb202 100644 --- a/Simulations/30e/6ee/30e6eedb46c2d313b709697ae73f0671c5079dc6/7aac3f64c8467f18f5265bc5aa63ed6895c348cf/README.yaml +++ b/Simulations/30e/6ee/30e6eedb46c2d313b709697ae73f0671c5079dc6/7aac3f64c8467f18f5265bc5aa63ed6895c348cf/README.yaml @@ -43,9 +43,13 @@ EXPERIMENT: C30: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/C30 (95:5) bilayer at 343 K (CHARMM36, GROMACS 2018.7, 100 ns) [NMRlipids simulation 756] + name: Molecular dynamics trajectory of a DPPC/C30 (95:5) bilayer at 343 K (CHARMM36, + GROMACS 2018.7, 100 ns) [NMRlipids simulation 756] alternateName: DPPC:C30(288:16)_T343K - description: Molecular dynamics trajectory of a lipid bilayer of 288 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 95 mol%) and 16 C30 (n-Triacontane, 5 mol%) at 343 K. Simulated with CHARMM36 in GROMACS 2018.7 for 100 ns (51875 atoms). Deposited as NMRlipids Databank simulation 756 and available from https://doi.org/10.5281/zenodo.7572990. + description: Molecular dynamics trajectory of a lipid bilayer of 288 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 95 mol%) and 16 C30 (n-Triacontane, 5 mol%) at 343 K. Simulated with CHARMM36 + in GROMACS 2018.7 for 100 ns (51875 atoms). Deposited as NMRlipids Databank simulation + 756 and available from https://doi.org/10.5281/zenodo.7572990. sameAs: https://doi.org/10.5281/zenodo.7572990 datePublished: '2023-01-26' license: @@ -137,7 +141,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.7572990 identifier: 10.5281/zenodo.7572990 url: https://doi.org/10.5281/zenodo.7572990 - name: 'MD simulation input files and results for ,,Atomistic MD simulations of n-alkanes in a phospholipid bilayer: CHARMM36 versus Slipids"' + name: 'MD simulation input files and results for ,,Atomistic MD simulations of + n-alkanes in a phospholipid bilayer: CHARMM36 versus Slipids"' publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/30e/6ee/30e6eedb46c2d313b709697ae73f0671c5079dc6/8af65c0b2b6d65d826aa4f88561c352a5f723df5/README.yaml b/Simulations/30e/6ee/30e6eedb46c2d313b709697ae73f0671c5079dc6/8af65c0b2b6d65d826aa4f88561c352a5f723df5/README.yaml index 4cc3732e80..e09cec50de 100644 --- a/Simulations/30e/6ee/30e6eedb46c2d313b709697ae73f0671c5079dc6/8af65c0b2b6d65d826aa4f88561c352a5f723df5/README.yaml +++ b/Simulations/30e/6ee/30e6eedb46c2d313b709697ae73f0671c5079dc6/8af65c0b2b6d65d826aa4f88561c352a5f723df5/README.yaml @@ -40,9 +40,13 @@ EXPERIMENT: C30: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/C30 (95:5) bilayer at 343 K (CHARMM36, GROMACS, 100 ns) [NMRlipids simulation 889] + name: Molecular dynamics trajectory of a DPPC/C30 (95:5) bilayer at 343 K (CHARMM36, + GROMACS, 100 ns) [NMRlipids simulation 889] alternateName: DPPC/C30 - description: Molecular dynamics trajectory of a lipid bilayer of 288 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 95 mol%) and 16 C30 (n-Triacontane, 5 mol%) at 343 K. Simulated with CHARMM36 in GROMACS for 100 ns (51875 atoms). Deposited as NMRlipids Databank simulation 889 and available from https://doi.org/10.5281/zenodo.7572990. + description: Molecular dynamics trajectory of a lipid bilayer of 288 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 95 mol%) and 16 C30 (n-Triacontane, 5 mol%) at 343 K. Simulated with CHARMM36 + in GROMACS for 100 ns (51875 atoms). Deposited as NMRlipids Databank simulation + 889 and available from https://doi.org/10.5281/zenodo.7572990. sameAs: https://doi.org/10.5281/zenodo.7572990 datePublished: '2023-01-26' license: @@ -134,7 +138,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.7572990 identifier: 10.5281/zenodo.7572990 url: https://doi.org/10.5281/zenodo.7572990 - name: 'MD simulation input files and results for ,,Atomistic MD simulations of n-alkanes in a phospholipid bilayer: CHARMM36 versus Slipids"' + name: 'MD simulation input files and results for ,,Atomistic MD simulations of + n-alkanes in a phospholipid bilayer: CHARMM36 versus Slipids"' publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/310/972/310972e588b9d3b8bb3049c5a4ee1977889c6559/a4d8e0ad017d67cfb566b576d573778c671c4cba/README.yaml b/Simulations/310/972/310972e588b9d3b8bb3049c5a4ee1977889c6559/a4d8e0ad017d67cfb566b576d573778c671c4cba/README.yaml index aea5086fb2..9196950d07 100644 --- a/Simulations/310/972/310972e588b9d3b8bb3049c5a4ee1977889c6559/a4d8e0ad017d67cfb566b576d573778c671c4cba/README.yaml +++ b/Simulations/310/972/310972e588b9d3b8bb3049c5a4ee1977889c6559/a4d8e0ad017d67cfb566b576d573778c671c4cba/README.yaml @@ -49,9 +49,13 @@ EXPERIMENT: - 10.1039/C4SM00066H/3 ID: 292 bioschema_properties: - name: Molecular dynamics trajectory of a POPS/SOD (50:50) bilayer at 298 K (MacRog, GROMACS, 100 ns) [NMRlipids simulation 292] + name: Molecular dynamics trajectory of a POPS/SOD (50:50) bilayer at 298 K (MacRog, + GROMACS, 100 ns) [NMRlipids simulation 292] alternateName: 128POPS_4480SOL_128SOD_298K_v1 - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 50 mol%) and 128 SOD (50 mol%) at 298 K. Simulated with MacRog in GROMACS for 100 ns (29824 atoms). Deposited as NMRlipids Databank simulation 292 and available from https://doi.org/10.5281/zenodo.1283335. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, + 50 mol%) and 128 SOD (50 mol%) at 298 K. Simulated with MacRog in GROMACS for + 100 ns (29824 atoms). Deposited as NMRlipids Databank simulation 292 and available + from https://doi.org/10.5281/zenodo.1283335. sameAs: https://doi.org/10.5281/zenodo.1283335 datePublished: '2018-06-05' license: @@ -143,7 +147,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1283335 identifier: 10.5281/zenodo.1283335 url: https://doi.org/10.5281/zenodo.1283335 - name: Macrog Pops Simulations (Versions 1 And 2) 298 K With Corrected Po Not Op Tails + name: Macrog Pops Simulations (Versions 1 And 2) 298 K With Corrected Po Not Op + Tails publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/316/a64/316a64f5998bd7d992ad0cdb264a7eb154dde78a/0f44a3751fd7025b7c3ad4a1898aeed7a6993624/README.yaml b/Simulations/316/a64/316a64f5998bd7d992ad0cdb264a7eb154dde78a/0f44a3751fd7025b7c3ad4a1898aeed7a6993624/README.yaml index 08a3f78f0d..1866737032 100644 --- a/Simulations/316/a64/316a64f5998bd7d992ad0cdb264a7eb154dde78a/0f44a3751fd7025b7c3ad4a1898aeed7a6993624/README.yaml +++ b/Simulations/316/a64/316a64f5998bd7d992ad0cdb264a7eb154dde78a/0f44a3751fd7025b7c3ad4a1898aeed7a6993624/README.yaml @@ -44,9 +44,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 295 bioschema_properties: - name: Molecular dynamics trajectory of a DOPS/SOD (50:50) bilayer at 303 K (CHARMM36, GROMACS, 100 ns) [NMRlipids simulation 295] + name: Molecular dynamics trajectory of a DOPS/SOD (50:50) bilayer at 303 K (CHARMM36, + GROMACS, 100 ns) [NMRlipids simulation 295] alternateName: 128DOPS_128SOD_4480SOL_303K_v1 - description: Molecular dynamics trajectory of a lipid bilayer of 128 DOPS (1,2-dioleoyl-sn-glycero-3-phospho-L-serine, 50 mol%) and 128 SOD (50 mol%) at 303 K. Simulated with CHARMM36 in GROMACS for 100 ns (30336 atoms). Deposited as NMRlipids Databank simulation 295 and available from https://doi.org/10.5281/zenodo.1129411. + description: Molecular dynamics trajectory of a lipid bilayer of 128 DOPS (1,2-dioleoyl-sn-glycero-3-phospho-L-serine, + 50 mol%) and 128 SOD (50 mol%) at 303 K. Simulated with CHARMM36 in GROMACS for + 100 ns (30336 atoms). Deposited as NMRlipids Databank simulation 295 and available + from https://doi.org/10.5281/zenodo.1129411. sameAs: https://doi.org/10.5281/zenodo.1129411 datePublished: '2017-12-24' license: diff --git a/Simulations/325/122/325122b1f8af70a4fc3001c4781c96773ca448ab/17740ef7cfae47602aece493a725deba4fdd47b8/README.yaml b/Simulations/325/122/325122b1f8af70a4fc3001c4781c96773ca448ab/17740ef7cfae47602aece493a725deba4fdd47b8/README.yaml index 6949ab2b82..110644bded 100644 --- a/Simulations/325/122/325122b1f8af70a4fc3001c4781c96773ca448ab/17740ef7cfae47602aece493a725deba4fdd47b8/README.yaml +++ b/Simulations/325/122/325122b1f8af70a4fc3001c4781c96773ca448ab/17740ef7cfae47602aece493a725deba4fdd47b8/README.yaml @@ -51,9 +51,13 @@ WARNINGS: PBC: z-jumps ID: 181 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (48:35:17) bilayer at 303 K (CHARMM36, GROMACS 4.5, 120 ns) [NMRlipids simulation 181] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (48:35:17) bilayer at 303 + K (CHARMM36, GROMACS 4.5, 120 ns) [NMRlipids simulation 181] alternateName: 72POPC_2164SOL_26CAL_52CLA_303K - description: Molecular dynamics trajectory of a lipid bilayer of 72 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 48 mol%), 52 CLA (35 mol%) and 26 CAL (17 mol%) at 303 K. Simulated with CHARMM36 in GROMACS 4.5 for 120 ns (16218 atoms). Deposited as NMRlipids Databank simulation 181 and available from https://doi.org/10.5281/zenodo.32570. + description: Molecular dynamics trajectory of a lipid bilayer of 72 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 48 mol%), 52 CLA (35 mol%) and 26 CAL (17 mol%) at 303 K. Simulated with CHARMM36 + in GROMACS 4.5 for 120 ns (16218 atoms). Deposited as NMRlipids Databank simulation + 181 and available from https://doi.org/10.5281/zenodo.32570. sameAs: https://doi.org/10.5281/zenodo.32570 datePublished: '2015-10-23' license: @@ -141,7 +145,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.32570 identifier: 10.5281/zenodo.32570 url: https://doi.org/10.5281/zenodo.32570 - name: Md Simulation Trajectory And Related Files For Popc Bilayer With 670Mm Cacl_2 (Charmm36, Gromacs 4.5) + name: Md Simulation Trajectory And Related Files For Popc Bilayer With 670Mm Cacl_2 + (Charmm36, Gromacs 4.5) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/32c/024/32c024dc50b77087ae85be6a2c51ed2fa6e5b652/a075886a44f6708716f997ce30055cf4ee8261a0/README.yaml b/Simulations/32c/024/32c024dc50b77087ae85be6a2c51ed2fa6e5b652/a075886a44f6708716f997ce30055cf4ee8261a0/README.yaml index 58d1bc6ed5..2deb060aec 100644 --- a/Simulations/32c/024/32c024dc50b77087ae85be6a2c51ed2fa6e5b652/a075886a44f6708716f997ce30055cf4ee8261a0/README.yaml +++ b/Simulations/32c/024/32c024dc50b77087ae85be6a2c51ed2fa6e5b652/a075886a44f6708716f997ce30055cf4ee8261a0/README.yaml @@ -47,9 +47,14 @@ EXPERIMENT: - 10.1016/j.bbamem.2011.07.022/4 ID: 267 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC bilayer at 323 K (Poger GROMOS 53A6_L; Reaction Field for computing electrostatics, GROMACS 4.0.7, 100 ns) [NMRlipids simulation 267] + name: Molecular dynamics trajectory of a DPPC bilayer at 323 K (Poger GROMOS 53A6_L; + Reaction Field for computing electrostatics, GROMACS 4.0.7, 100 ns) [NMRlipids + simulation 267] alternateName: 128DPPC_5841SOL_323K - description: Molecular dynamics trajectory of a lipid bilayer of 128 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) at 323 K. Simulated with Poger GROMOS 53A6_L; Reaction Field for computing electrostatics in GROMACS 4.0.7 for 100 ns (23923 atoms). Deposited as NMRlipids Databank simulation 267 and available from https://doi.org/10.5281/zenodo.14592. + description: Molecular dynamics trajectory of a lipid bilayer of 128 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) + at 323 K. Simulated with Poger GROMOS 53A6_L; Reaction Field for computing electrostatics + in GROMACS 4.0.7 for 100 ns (23923 atoms). Deposited as NMRlipids Databank simulation + 267 and available from https://doi.org/10.5281/zenodo.14592. sameAs: https://doi.org/10.5281/zenodo.14592 datePublished: '2015-01-27' license: @@ -141,7 +146,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.14592 identifier: 10.5281/zenodo.14592 url: https://doi.org/10.5281/zenodo.14592 - name: Md Simulation Trajectory And Related Files For Dppc Bilayer In Full Hydration (Poger Gromos 53A6_L, Gromacs 4.0.7, Reaction Field, Traj 1) + name: Md Simulation Trajectory And Related Files For Dppc Bilayer In Full Hydration + (Poger Gromos 53A6_L, Gromacs 4.0.7, Reaction Field, Traj 1) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/334/7d6/3347d64644484425bb2f2e7d7f7aeceb953e1c67/ac59d986b3e7e1aa87d6a340f486447be9108713/README.yaml b/Simulations/334/7d6/3347d64644484425bb2f2e7d7f7aeceb953e1c67/ac59d986b3e7e1aa87d6a340f486447be9108713/README.yaml index e466cdc73e..e2bbb01553 100644 --- a/Simulations/334/7d6/3347d64644484425bb2f2e7d7f7aeceb953e1c67/ac59d986b3e7e1aa87d6a340f486447be9108713/README.yaml +++ b/Simulations/334/7d6/3347d64644484425bb2f2e7d7f7aeceb953e1c67/ac59d986b3e7e1aa87d6a340f486447be9108713/README.yaml @@ -38,9 +38,12 @@ EXPERIMENT: FORMFACTOR: - 10.1016/j.bbamem.2011.07.022/6 bioschema_properties: - name: Molecular dynamics trajectory of a DLPC bilayer at 293 K (CHARMM36/LJ-PME, GROMACS Gromacs 2022, 100 ns) [NMRlipids simulation 913] + name: Molecular dynamics trajectory of a DLPC bilayer at 293 K (CHARMM36/LJ-PME, + GROMACS Gromacs 2022, 100 ns) [NMRlipids simulation 913] alternateName: Fully hydrated DLPC bilayer in SPC/E water - description: Molecular dynamics trajectory of a lipid bilayer of 100 DLPC (1,2-dilauroyl-sn-glycero-3-phosphocholine) at 293 K. Simulated with CHARMM36/LJ-PME in GROMACS Gromacs 2022 for 100 ns (23542 atoms). Deposited as NMRlipids Databank simulation 913 and available from https://doi.org/10.5281/zenodo.20579050. + description: Molecular dynamics trajectory of a lipid bilayer of 100 DLPC (1,2-dilauroyl-sn-glycero-3-phosphocholine) + at 293 K. Simulated with CHARMM36/LJ-PME in GROMACS Gromacs 2022 for 100 ns (23542 + atoms). Deposited as NMRlipids Databank simulation 913 and available from https://doi.org/10.5281/zenodo.20579050. sameAs: https://doi.org/10.5281/zenodo.20579050 datePublished: '2026-06-07' license: @@ -131,7 +134,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.20579050 identifier: 10.5281/zenodo.20579050 url: https://doi.org/10.5281/zenodo.20579050 - name: Fully hydrated DLPC bilayer at different temperatures simulated using CHARMM36 with LJ-PME and LJ-cutoff + name: Fully hydrated DLPC bilayer at different temperatures simulated using CHARMM36 + with LJ-PME and LJ-cutoff publisher: Zenodo _source: api: datacite diff --git a/Simulations/341/55f/34155fc126221f6d9eca9ea4d261035c126917d7/0a2440d47f171355cdf0d282f471de7fee7bbd0e/README.yaml b/Simulations/341/55f/34155fc126221f6d9eca9ea4d261035c126917d7/0a2440d47f171355cdf0d282f471de7fee7bbd0e/README.yaml index 1a4bd13d28..1a75f9c77d 100644 --- a/Simulations/341/55f/34155fc126221f6d9eca9ea4d261035c126917d7/0a2440d47f171355cdf0d282f471de7fee7bbd0e/README.yaml +++ b/Simulations/341/55f/34155fc126221f6d9eca9ea4d261035c126917d7/0a2440d47f171355cdf0d282f471de7fee7bbd0e/README.yaml @@ -44,9 +44,12 @@ EXPERIMENT: DRPC: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a DRPC bilayer at 333.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 629] + name: Molecular dynamics trajectory of a DRPC bilayer at 333.15 K (CHARMM36, GROMACS, + 1001 ns) [NMRlipids simulation 629] alternateName: 256DRPC_12800SOL_333K - description: Molecular dynamics trajectory of a lipid bilayer of 256 DRPC (1,2-(14:1$^\Delta9$)-sn-glycero-3-phosphocholine) at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (67584 atoms). Deposited as NMRlipids Databank simulation 629 and available from https://doi.org/10.5281/zenodo.6943413. + description: Molecular dynamics trajectory of a lipid bilayer of 256 DRPC (1,2-(14:1$^\Delta9$)-sn-glycero-3-phosphocholine) + at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (67584 atoms). Deposited + as NMRlipids Databank simulation 629 and available from https://doi.org/10.5281/zenodo.6943413. sameAs: https://doi.org/10.5281/zenodo.6943413 datePublished: '2022-07-30' license: @@ -134,7 +137,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.6943413 identifier: 10.5281/zenodo.6943413 url: https://doi.org/10.5281/zenodo.6943413 - name: Simulations of different single-component bilayers, three different system sizes + name: Simulations of different single-component bilayers, three different system + sizes publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/347/ae8/347ae8a9b0e8351a27c87337326ecfad6bc623cf/345e7a2be94a2692fec298aeccc31e44b29c38d3/README.yaml b/Simulations/347/ae8/347ae8a9b0e8351a27c87337326ecfad6bc623cf/345e7a2be94a2692fec298aeccc31e44b29c38d3/README.yaml index 1b7d283b94..b163b99049 100644 --- a/Simulations/347/ae8/347ae8a9b0e8351a27c87337326ecfad6bc623cf/345e7a2be94a2692fec298aeccc31e44b29c38d3/README.yaml +++ b/Simulations/347/ae8/347ae8a9b0e8351a27c87337326ecfad6bc623cf/345e7a2be94a2692fec298aeccc31e44b29c38d3/README.yaml @@ -48,9 +48,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 871 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (38:31:31) bilayer at 300 K (OPLS3e, GROMACS Desmond of Schrödinger 2019-4, 900 ns) [NMRlipids simulation 871] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (38:31:31) bilayer at 300 + K (OPLS3e, GROMACS Desmond of Schrödinger 2019-4, 900 ns) [NMRlipids simulation + 871] alternateName: POPC, 44 w/l, 300 K, 1 M NaCl - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 38 mol%), 160 CLA (31 mol%) and 160 SOD (31 mol%) at 300 K. Simulated with OPLS3e in GROMACS Desmond of Schrödinger 2019-4 for 900 ns (53760 atoms). Deposited as NMRlipids Databank simulation 871 and available from https://doi.org/10.5281/zenodo.10184815. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 38 mol%), 160 CLA (31 mol%) and 160 SOD (31 mol%) at 300 K. Simulated with OPLS3e + in GROMACS Desmond of Schrödinger 2019-4 for 900 ns (53760 atoms). Deposited as + NMRlipids Databank simulation 871 and available from https://doi.org/10.5281/zenodo.10184815. sameAs: https://doi.org/10.5281/zenodo.10184815 datePublished: '2022' license: @@ -141,7 +146,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.10184815 identifier: 10.5281/zenodo.10184815 url: https://doi.org/10.5281/zenodo.10184815 - name: MD simulation of POPC bilayer with OPLS3e force field, 1000 mM NaCl part 1 + name: MD simulation of POPC bilayer with OPLS3e force field, 1000 mM NaCl part + 1 publisher: Zenodo _source: api: datacite diff --git a/Simulations/350/344/3503448a077324dc2e7ef7c943307a0394157eae/1e46927841db56a38da6bd532fa449e3cf72a8fe/README.yaml b/Simulations/350/344/3503448a077324dc2e7ef7c943307a0394157eae/1e46927841db56a38da6bd532fa449e3cf72a8fe/README.yaml index d76c22c5e4..925c119812 100644 --- a/Simulations/350/344/3503448a077324dc2e7ef7c943307a0394157eae/1e46927841db56a38da6bd532fa449e3cf72a8fe/README.yaml +++ b/Simulations/350/344/3503448a077324dc2e7ef7c943307a0394157eae/1e46927841db56a38da6bd532fa449e3cf72a8fe/README.yaml @@ -57,9 +57,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 142 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/DHMDMAB (42:29:29) bilayer at 313 K (ECC-lipids, GROMACS 5.1.4, 200 ns) [NMRlipids simulation 142] + name: Molecular dynamics trajectory of a POPC/CLA/DHMDMAB (42:29:29) bilayer at + 313 K (ECC-lipids, GROMACS 5.1.4, 200 ns) [NMRlipids simulation 142] alternateName: 100POPC_6214SOL_70DHMDMAB_70CLA_313K_SPCEmodel - description: Molecular dynamics trajectory of a lipid bilayer of 100 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 42 mol%), 70 CLA (29 mol%) and 70 DHMDMAB (dihexadecyldimethylammonium, 29 mol%) at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 200 ns (39602 atoms). Deposited as NMRlipids Databank simulation 142 and available from https://doi.org/10.5281/zenodo.1118682. + description: Molecular dynamics trajectory of a lipid bilayer of 100 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 42 mol%), 70 CLA (29 mol%) and 70 DHMDMAB (dihexadecyldimethylammonium, 29 mol%) + at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 200 ns (39602 atoms). + Deposited as NMRlipids Databank simulation 142 and available from https://doi.org/10.5281/zenodo.1118682. sameAs: https://doi.org/10.5281/zenodo.1118682 datePublished: '2017-12-19' license: @@ -150,7 +154,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1118682 identifier: 10.5281/zenodo.1118682 url: https://doi.org/10.5281/zenodo.1118682 - name: Simulations Of Popc Lipid Bilayer In Water Solution With Various Molar Fractions Of Cationic Surfactant Dihexadecylammonium Using Ecc-Popc Force Field + name: Simulations Of Popc Lipid Bilayer In Water Solution With Various Molar Fractions + Of Cationic Surfactant Dihexadecylammonium Using Ecc-Popc Force Field publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/351/942/3519421ff6c7df40e1da7ac6b6e9ea4d06c911ca/1419f364222a22aadc90d4ec0963e18173e1df2a/README.yaml b/Simulations/351/942/3519421ff6c7df40e1da7ac6b6e9ea4d06c911ca/1419f364222a22aadc90d4ec0963e18173e1df2a/README.yaml index 5ebd63582b..6b0c910996 100644 --- a/Simulations/351/942/3519421ff6c7df40e1da7ac6b6e9ea4d06c911ca/1419f364222a22aadc90d4ec0963e18173e1df2a/README.yaml +++ b/Simulations/351/942/3519421ff6c7df40e1da7ac6b6e9ea4d06c911ca/1419f364222a22aadc90d4ec0963e18173e1df2a/README.yaml @@ -53,9 +53,13 @@ EXPERIMENT: - 10.1039/C4SM00066H/3 ID: 473 bioschema_properties: - name: Molecular dynamics trajectory of a POPS/SOD (50:50) bilayer at 298 K (GROMOS-CKP, GROMOS NH3 charges and PME, GROMACS, 100 ns) [NMRlipids simulation 473] + name: Molecular dynamics trajectory of a POPS/SOD (50:50) bilayer at 298 K (GROMOS-CKP, + GROMOS NH3 charges and PME, GROMACS, 100 ns) [NMRlipids simulation 473] alternateName: 128POPS_4480SOL_128SOD_298K_GROMOS-CKP_v2 - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 50 mol%) and 128 SOD (50 mol%) at 298 K. Simulated with GROMOS-CKP, GROMOS NH3 charges and PME in GROMACS for 100 ns (20608 atoms). Deposited as NMRlipids Databank simulation 473 and available from https://doi.org/10.5281/zenodo.1129435. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, + 50 mol%) and 128 SOD (50 mol%) at 298 K. Simulated with GROMOS-CKP, GROMOS NH3 + charges and PME in GROMACS for 100 ns (20608 atoms). Deposited as NMRlipids Databank + simulation 473 and available from https://doi.org/10.5281/zenodo.1129435. sameAs: https://doi.org/10.5281/zenodo.1129435 datePublished: '2017-12-24' license: @@ -148,7 +152,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1129435 identifier: 10.5281/zenodo.1129435 url: https://doi.org/10.5281/zenodo.1129435 - name: Gromos-Ckp Pops Simulations (Versions 1 And 2) 298 K With Gromos Nh3 Charges And Pme + name: Gromos-Ckp Pops Simulations (Versions 1 And 2) 298 K With Gromos Nh3 Charges + And Pme publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/354/c96/354c960d52ae3ede20ac62f39f791a4ba9892659/b73fc91c765a75d02c0c9fbc87e400dc79221c44/README.yaml b/Simulations/354/c96/354c960d52ae3ede20ac62f39f791a4ba9892659/b73fc91c765a75d02c0c9fbc87e400dc79221c44/README.yaml index d4ec77f545..093628e986 100644 --- a/Simulations/354/c96/354c960d52ae3ede20ac62f39f791a4ba9892659/b73fc91c765a75d02c0c9fbc87e400dc79221c44/README.yaml +++ b/Simulations/354/c96/354c960d52ae3ede20ac62f39f791a4ba9892659/b73fc91c765a75d02c0c9fbc87e400dc79221c44/README.yaml @@ -40,9 +40,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 124 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 298 K (MacRog, GROMACS 4.5.5, 50 ns) [NMRlipids simulation 124] + name: Molecular dynamics trajectory of a POPC bilayer at 298 K (MacRog, GROMACS + 4.5.5, 50 ns) [NMRlipids simulation 124] alternateName: 288POPC_2880SOL_298K - description: Molecular dynamics trajectory of a lipid bilayer of 288 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 298 K. Simulated with MacRog in GROMACS 4.5.5 for 50 ns (47232 atoms). Deposited as NMRlipids Databank simulation 124 and available from https://doi.org/10.5281/zenodo.13498. + description: Molecular dynamics trajectory of a lipid bilayer of 288 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 298 K. Simulated with MacRog in GROMACS 4.5.5 for 50 ns (47232 atoms). Deposited + as NMRlipids Databank simulation 124 and available from https://doi.org/10.5281/zenodo.13498. sameAs: https://doi.org/10.5281/zenodo.13498 datePublished: '2014-12-30' license: diff --git a/Simulations/35d/d6b/35dd6bcb5bf03400b81c070292e36025c48dc1a6/3d0ca721c24d7f22d09178f10f1dd89a333dfe07/README.yaml b/Simulations/35d/d6b/35dd6bcb5bf03400b81c070292e36025c48dc1a6/3d0ca721c24d7f22d09178f10f1dd89a333dfe07/README.yaml index dc1a10c4da..9ecd780378 100644 --- a/Simulations/35d/d6b/35dd6bcb5bf03400b81c070292e36025c48dc1a6/3d0ca721c24d7f22d09178f10f1dd89a333dfe07/README.yaml +++ b/Simulations/35d/d6b/35dd6bcb5bf03400b81c070292e36025c48dc1a6/3d0ca721c24d7f22d09178f10f1dd89a333dfe07/README.yaml @@ -42,9 +42,12 @@ TOP: DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 261 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 310 K (GROMOS-CKP, GROMACS 2018.3, 100 ns) [NMRlipids simulation 261] + name: Molecular dynamics trajectory of a POPC bilayer at 310 K (GROMOS-CKP, GROMACS + 2018.3, 100 ns) [NMRlipids simulation 261] alternateName: POPC_T310K - description: Molecular dynamics trajectory of a lipid bilayer of 500 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 310 K. Simulated with GROMOS-CKP in GROMACS 2018.3 for 100 ns (101000 atoms). Deposited as NMRlipids Databank simulation 261 and available from https://doi.org/10.5281/zenodo.3247435. + description: Molecular dynamics trajectory of a lipid bilayer of 500 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 310 K. Simulated with GROMOS-CKP in GROMACS 2018.3 for 100 ns (101000 atoms). + Deposited as NMRlipids Databank simulation 261 and available from https://doi.org/10.5281/zenodo.3247435. sameAs: https://doi.org/10.5281/zenodo.3247435 datePublished: '2019-06-17' license: diff --git a/Simulations/362/268/3622689c85bc136ccf4994393169397be60cf78c/1f7e1dad9437bb7a66690d0ae8b3e1174b48b467/README.yaml b/Simulations/362/268/3622689c85bc136ccf4994393169397be60cf78c/1f7e1dad9437bb7a66690d0ae8b3e1174b48b467/README.yaml index a49d48654b..d81b546bcf 100644 --- a/Simulations/362/268/3622689c85bc136ccf4994393169397be60cf78c/1f7e1dad9437bb7a66690d0ae8b3e1174b48b467/README.yaml +++ b/Simulations/362/268/3622689c85bc136ccf4994393169397be60cf78c/1f7e1dad9437bb7a66690d0ae8b3e1174b48b467/README.yaml @@ -63,9 +63,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 260 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL/POPS/SOD (49:21:11:10:10) bilayer at 298 K (ECC-lipids, SPC/E water model, ECC-ions, GROMACS 2018.0, 1328 ns) [NMRlipids simulation 260] + name: Molecular dynamics trajectory of a POPC/CLA/CAL/POPS/SOD (49:21:11:10:10) + bilayer at 298 K (ECC-lipids, SPC/E water model, ECC-ions, GROMACS 2018.0, 1328 + ns) [NMRlipids simulation 260] alternateName: 12POPS_60POPC_3561SOL_13CAL_26CLA_12SOD_298K - description: Molecular dynamics trajectory of a lipid bilayer of 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 49 mol%), 26 CLA (21 mol%), 13 CAL (11 mol%), 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 10 mol%) and 12 SOD (10 mol%) at 298 K. Simulated with ECC-lipids, SPC/E water model, ECC-ions in GROMACS 2018.0 for 1328 ns (20298 atoms). Deposited as NMRlipids Databank simulation 260 and available from https://doi.org/10.5281/zenodo.1488102. + description: Molecular dynamics trajectory of a lipid bilayer of 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 49 mol%), 26 CLA (21 mol%), 13 CAL (11 mol%), 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, + 10 mol%) and 12 SOD (10 mol%) at 298 K. Simulated with ECC-lipids, SPC/E water + model, ECC-ions in GROMACS 2018.0 for 1328 ns (20298 atoms). Deposited as NMRlipids + Databank simulation 260 and available from https://doi.org/10.5281/zenodo.1488102. sameAs: https://doi.org/10.5281/zenodo.1488102 datePublished: '2018-11-14' license: @@ -158,7 +164,9 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1488102 identifier: 10.5281/zenodo.1488102 url: https://doi.org/10.5281/zenodo.1488102 - name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS (5:1) with ECC-lipids force field, and Na+ (K+) counterions at various CaCl2 additional concentrations + name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS + (5:1) with ECC-lipids force field, and Na+ (K+) counterions at various CaCl2 + additional concentrations publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/363/f08/363f08e91a530262e31f644cb4cbae005e81d780/56713ad1f468d3999034adbaa151a942f371ca2f/README.yaml b/Simulations/363/f08/363f08e91a530262e31f644cb4cbae005e81d780/56713ad1f468d3999034adbaa151a942f371ca2f/README.yaml index 9820ba66f3..707b957ca2 100644 --- a/Simulations/363/f08/363f08e91a530262e31f644cb4cbae005e81d780/56713ad1f468d3999034adbaa151a942f371ca2f/README.yaml +++ b/Simulations/363/f08/363f08e91a530262e31f644cb4cbae005e81d780/56713ad1f468d3999034adbaa151a942f371ca2f/README.yaml @@ -45,9 +45,12 @@ EXPERIMENT: - unpublished/nesterenkoDMPCbOG/1 FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a DMPC bilayer at 313.15 K (Charmm36, GROMACS 2022.5, 539 ns) [NMRlipids simulation 789] + name: Molecular dynamics trajectory of a DMPC bilayer at 313.15 K (Charmm36, GROMACS + 2022.5, 539 ns) [NMRlipids simulation 789] alternateName: DMPC(313K,pme) - description: Molecular dynamics trajectory of a lipid bilayer of 64 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) at 313.15 K. Simulated with Charmm36 in GROMACS 2022.5 for 539 ns (17152 atoms). Deposited as NMRlipids Databank simulation 789 and available from https://doi.org/10.5281/zenodo.8431710. + description: Molecular dynamics trajectory of a lipid bilayer of 64 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) + at 313.15 K. Simulated with Charmm36 in GROMACS 2022.5 for 539 ns (17152 atoms). + Deposited as NMRlipids Databank simulation 789 and available from https://doi.org/10.5281/zenodo.8431710. sameAs: https://doi.org/10.5281/zenodo.8431710 datePublished: '2023-10-11' license: diff --git a/Simulations/36e/333/36e333d9de810fdc8d0009df0e755225f7645161/36e333d9de810fdc8d0009df0e755225f7645161/README.yaml b/Simulations/36e/333/36e333d9de810fdc8d0009df0e755225f7645161/36e333d9de810fdc8d0009df0e755225f7645161/README.yaml index e327ecda34..cec8b7146c 100644 --- a/Simulations/36e/333/36e333d9de810fdc8d0009df0e755225f7645161/36e333d9de810fdc8d0009df0e755225f7645161/README.yaml +++ b/Simulations/36e/333/36e333d9de810fdc8d0009df0e755225f7645161/36e333d9de810fdc8d0009df0e755225f7645161/README.yaml @@ -46,9 +46,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 735 bioschema_properties: - name: Molecular dynamics trajectory of a DOPC/CLA/SOD (68:16:16) bilayer at 303 K (AMOEBA, OPENMM v7.5.1, 218 ns) [NMRlipids simulation 735] + name: Molecular dynamics trajectory of a DOPC/CLA/SOD (68:16:16) bilayer at 303 + K (AMOEBA, OPENMM v7.5.1, 218 ns) [NMRlipids simulation 735] alternateName: DOPC_450mM_NaCl_at_303K_with_AMOEBA - description: Molecular dynamics trajectory of a lipid bilayer of 72 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, 68 mol%), 17 CLA (16 mol%) and 17 SOD (16 mol%) at 303 K. Simulated with AMOEBA in OPENMM v7.5.1 for 218 ns (18610 atoms). Deposited as NMRlipids Databank simulation 735 and available from https://doi.org/10.5281/zenodo.7604711. + description: Molecular dynamics trajectory of a lipid bilayer of 72 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, + 68 mol%), 17 CLA (16 mol%) and 17 SOD (16 mol%) at 303 K. Simulated with AMOEBA + in OPENMM v7.5.1 for 218 ns (18610 atoms). Deposited as NMRlipids Databank simulation + 735 and available from https://doi.org/10.5281/zenodo.7604711. sameAs: https://doi.org/10.5281/zenodo.7604711 datePublished: '2022-12-09' license: @@ -136,7 +140,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.7604711 identifier: 10.5281/zenodo.7604711 url: https://doi.org/10.5281/zenodo.7604711 - name: MD Simulation data for a pure DOPC bilayer (450 mM NaCl) with AMOEBA force field + OpenMM + name: MD Simulation data for a pure DOPC bilayer (450 mM NaCl) with AMOEBA force + field + OpenMM publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/370/8fe/3708fe5639902a0ec0b60ba2c4fdb7711184c6bb/a15498a0795561646a76b01370ec8fd493593df4/README.yaml b/Simulations/370/8fe/3708fe5639902a0ec0b60ba2c4fdb7711184c6bb/a15498a0795561646a76b01370ec8fd493593df4/README.yaml index 4e0f19ef9d..8630c3393d 100644 --- a/Simulations/370/8fe/3708fe5639902a0ec0b60ba2c4fdb7711184c6bb/a15498a0795561646a76b01370ec8fd493593df4/README.yaml +++ b/Simulations/370/8fe/3708fe5639902a0ec0b60ba2c4fdb7711184c6bb/a15498a0795561646a76b01370ec8fd493593df4/README.yaml @@ -51,9 +51,13 @@ WARNINGS: PBC: z-jumps ID: 544 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (73:13:13) bilayer at 303 K (CHARMM36, GROMACS 4.5, 60 ns) [NMRlipids simulation 544] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (73:13:13) bilayer at 303 + K (CHARMM36, GROMACS 4.5, 60 ns) [NMRlipids simulation 544] alternateName: 72POPC_2085SOL_13CLA_13NA_303K - description: Molecular dynamics trajectory of a lipid bilayer of 72 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 73 mol%), 13 CLA (13 mol%) and 13 SOD (13 mol%) at 303 K. Simulated with CHARMM36 in GROMACS 4.5 for 60 ns (15929 atoms). Deposited as NMRlipids Databank simulation 544 and available from https://doi.org/10.5281/zenodo.4750862. + description: Molecular dynamics trajectory of a lipid bilayer of 72 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 73 mol%), 13 CLA (13 mol%) and 13 SOD (13 mol%) at 303 K. Simulated with CHARMM36 + in GROMACS 4.5 for 60 ns (15929 atoms). Deposited as NMRlipids Databank simulation + 544 and available from https://doi.org/10.5281/zenodo.4750862. sameAs: https://doi.org/10.5281/zenodo.4750862 datePublished: '2015-10-21' license: @@ -141,7 +145,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.4750862 identifier: 10.5281/zenodo.4750862 url: https://doi.org/10.5281/zenodo.4750862 - name: MD simulation trajectory and related files for POPC bilayer with 350mM NaCl (CHARMM36, Gromacs 4.5) + name: MD simulation trajectory and related files for POPC bilayer with 350mM NaCl + (CHARMM36, Gromacs 4.5) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/371/d53/371d534a1bb41fd81e137717e473e6916c9bbf70/7c24007a3d9cbe605a31999850e929ebfaf530f7/README.yaml b/Simulations/371/d53/371d534a1bb41fd81e137717e473e6916c9bbf70/7c24007a3d9cbe605a31999850e929ebfaf530f7/README.yaml index 469ae946ba..23d63eb16f 100644 --- a/Simulations/371/d53/371d534a1bb41fd81e137717e473e6916c9bbf70/7c24007a3d9cbe605a31999850e929ebfaf530f7/README.yaml +++ b/Simulations/371/d53/371d534a1bb41fd81e137717e473e6916c9bbf70/7c24007a3d9cbe605a31999850e929ebfaf530f7/README.yaml @@ -49,9 +49,13 @@ EXPERIMENT: - 10.1039/C4SM00066H/3 ID: 26 bioschema_properties: - name: Molecular dynamics trajectory of a POPS/SOD (50:50) bilayer at 298 K (MacRog, GROMACS, 100 ns) [NMRlipids simulation 26] + name: Molecular dynamics trajectory of a POPS/SOD (50:50) bilayer at 298 K (MacRog, + GROMACS, 100 ns) [NMRlipids simulation 26] alternateName: 128POPS_4480SOL_128SOD_298K_v2 - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 50 mol%) and 128 SOD (50 mol%) at 298 K. Simulated with MacRog in GROMACS for 100 ns (29824 atoms). Deposited as NMRlipids Databank simulation 26 and available from https://doi.org/10.5281/zenodo.1283335. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, + 50 mol%) and 128 SOD (50 mol%) at 298 K. Simulated with MacRog in GROMACS for + 100 ns (29824 atoms). Deposited as NMRlipids Databank simulation 26 and available + from https://doi.org/10.5281/zenodo.1283335. sameAs: https://doi.org/10.5281/zenodo.1283335 datePublished: '2018-06-05' license: @@ -143,7 +147,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1283335 identifier: 10.5281/zenodo.1283335 url: https://doi.org/10.5281/zenodo.1283335 - name: Macrog Pops Simulations (Versions 1 And 2) 298 K With Corrected Po Not Op Tails + name: Macrog Pops Simulations (Versions 1 And 2) 298 K With Corrected Po Not Op + Tails publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/372/817/3728174b1be9613822cc98a979dcdac176e057c4/9559e5c7df710415a2df60fc78de76d3a78d7699/README.yaml b/Simulations/372/817/3728174b1be9613822cc98a979dcdac176e057c4/9559e5c7df710415a2df60fc78de76d3a78d7699/README.yaml index 3c07bd1ff4..cb0cf214ba 100644 --- a/Simulations/372/817/3728174b1be9613822cc98a979dcdac176e057c4/9559e5c7df710415a2df60fc78de76d3a78d7699/README.yaml +++ b/Simulations/372/817/3728174b1be9613822cc98a979dcdac176e057c4/9559e5c7df710415a2df60fc78de76d3a78d7699/README.yaml @@ -47,9 +47,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 64 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPE (50:50) bilayer at 300 K (CHARMM36, GROMACS, 300 ns) [NMRlipids simulation 64] + name: Molecular dynamics trajectory of a POPC/POPE (50:50) bilayer at 300 K (CHARMM36, + GROMACS, 300 ns) [NMRlipids simulation 64] alternateName: 128POPC_128POPE_9102SOL_300K - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 50 mol%) and 128 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 50 mol%) at 300 K. Simulated with CHARMM36 in GROMACS for 300 ns (60458 atoms). Deposited as NMRlipids Databank simulation 64 and available from https://doi.org/10.5281/zenodo.1306821. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 50 mol%) and 128 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, + 50 mol%) at 300 K. Simulated with CHARMM36 in GROMACS for 300 ns (60458 atoms). + Deposited as NMRlipids Databank simulation 64 and available from https://doi.org/10.5281/zenodo.1306821. sameAs: https://doi.org/10.5281/zenodo.1306821 datePublished: '2018-07-06' license: diff --git a/Simulations/372/a91/372a917a2f528473eef642569a4c4f5f7472d473/e23ae04f10840187c2cf50c92451226d6bbadf63/README.yaml b/Simulations/372/a91/372a917a2f528473eef642569a4c4f5f7472d473/e23ae04f10840187c2cf50c92451226d6bbadf63/README.yaml index 0f29f7162f..b8e0d87921 100644 --- a/Simulations/372/a91/372a917a2f528473eef642569a4c4f5f7472d473/e23ae04f10840187c2cf50c92451226d6bbadf63/README.yaml +++ b/Simulations/372/a91/372a917a2f528473eef642569a4c4f5f7472d473/e23ae04f10840187c2cf50c92451226d6bbadf63/README.yaml @@ -45,9 +45,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 65 bioschema_properties: - name: Molecular dynamics trajectory of a DOPE bilayer at 271 K (Berger-DOPE-2004, GROMACS 4.0.7, 100 ns) [NMRlipids simulation 65] + name: Molecular dynamics trajectory of a DOPE bilayer at 271 K (Berger-DOPE-2004, + GROMACS 4.0.7, 100 ns) [NMRlipids simulation 65] alternateName: 128DOPE_4789SOL_271K_v2 - description: Molecular dynamics trajectory of a lipid bilayer of 128 DOPE (1,2-dioleoyl-sn-glycero-3-phosphoethanolamine) at 271 K. Simulated with Berger-DOPE-2004 in GROMACS 4.0.7 for 100 ns (21279 atoms). Deposited as NMRlipids Databank simulation 65 and available from https://doi.org/10.5281/zenodo.1293928. + description: Molecular dynamics trajectory of a lipid bilayer of 128 DOPE (1,2-dioleoyl-sn-glycero-3-phosphoethanolamine) + at 271 K. Simulated with Berger-DOPE-2004 in GROMACS 4.0.7 for 100 ns (21279 atoms). + Deposited as NMRlipids Databank simulation 65 and available from https://doi.org/10.5281/zenodo.1293928. sameAs: https://doi.org/10.5281/zenodo.1293928 datePublished: '2018-06-20' license: diff --git a/Simulations/387/6d8/3876d878edf3efd6e4b40a7e78661581b1dfd387/b048d322ae8d7ee95e888b26f87dda3ec6fd9350/README.yaml b/Simulations/387/6d8/3876d878edf3efd6e4b40a7e78661581b1dfd387/b048d322ae8d7ee95e888b26f87dda3ec6fd9350/README.yaml index 6f59f7520d..207b6096f0 100644 --- a/Simulations/387/6d8/3876d878edf3efd6e4b40a7e78661581b1dfd387/b048d322ae8d7ee95e888b26f87dda3ec6fd9350/README.yaml +++ b/Simulations/387/6d8/3876d878edf3efd6e4b40a7e78661581b1dfd387/b048d322ae8d7ee95e888b26f87dda3ec6fd9350/README.yaml @@ -52,9 +52,13 @@ EXPERIMENT: CHOL: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a POPE/CHOL/DOG (58:33:9) bilayer at 310 K (Lipid17, GROMACS 18.7, 1000 ns) [NMRlipids simulation 718] + name: Molecular dynamics trajectory of a POPE/CHOL/DOG (58:33:9) bilayer at 310 + K (Lipid17, GROMACS 18.7, 1000 ns) [NMRlipids simulation 718] alternateName: DOGandCHOLinPOPEwithLipid17 - description: Molecular dynamics trajectory of a lipid bilayer of 74 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 58 mol%), 42 CHOL (cholesterol, 33 mol%) and 12 DOG (1,2-dioleoyl-sn-glycerol, 9 mol%) at 310 K. Simulated with Lipid17 in GROMACS 18.7 for 1000 ns (32950 atoms). Deposited as NMRlipids Databank simulation 718 and available from https://doi.org/10.5281/zenodo.6822850. + description: Molecular dynamics trajectory of a lipid bilayer of 74 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, + 58 mol%), 42 CHOL (cholesterol, 33 mol%) and 12 DOG (1,2-dioleoyl-sn-glycerol, + 9 mol%) at 310 K. Simulated with Lipid17 in GROMACS 18.7 for 1000 ns (32950 atoms). + Deposited as NMRlipids Databank simulation 718 and available from https://doi.org/10.5281/zenodo.6822850. sameAs: https://doi.org/10.5281/zenodo.6822850 datePublished: '2022-07-12' license: diff --git a/Simulations/38a/8c9/38a8c9a8a4f9c96650dcc36bafd8fc6edf25d086/4c82a38598f628ed5bd34f27e24ea11ce730752f/README.yaml b/Simulations/38a/8c9/38a8c9a8a4f9c96650dcc36bafd8fc6edf25d086/4c82a38598f628ed5bd34f27e24ea11ce730752f/README.yaml index a2ccd1bcf6..26f1f91d86 100644 --- a/Simulations/38a/8c9/38a8c9a8a4f9c96650dcc36bafd8fc6edf25d086/4c82a38598f628ed5bd34f27e24ea11ce730752f/README.yaml +++ b/Simulations/38a/8c9/38a8c9a8a4f9c96650dcc36bafd8fc6edf25d086/4c82a38598f628ed5bd34f27e24ea11ce730752f/README.yaml @@ -48,9 +48,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 340 bioschema_properties: - name: Molecular dynamics trajectory of a POPS/POT (50:50) bilayer at 298 K (ECC-lipids, SPC water model, ECC-ions, GROMACS 2018.0, 956 ns) [NMRlipids simulation 340] + name: Molecular dynamics trajectory of a POPS/POT (50:50) bilayer at 298 K (ECC-lipids, + SPC water model, ECC-ions, GROMACS 2018.0, 956 ns) [NMRlipids simulation 340] alternateName: 72POPS_3600SOL_72POT_298K_ECC-lipid - description: Molecular dynamics trajectory of a lipid bilayer of 72 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 50 mol%) and 72 POT (50 mol%) at 298 K. Simulated with ECC-lipids, SPC water model, ECC-ions in GROMACS 2018.0 for 956 ns (20016 atoms). Deposited as NMRlipids Databank simulation 340 and available from https://doi.org/10.5281/zenodo.1488094. + description: Molecular dynamics trajectory of a lipid bilayer of 72 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, + 50 mol%) and 72 POT (50 mol%) at 298 K. Simulated with ECC-lipids, SPC water model, + ECC-ions in GROMACS 2018.0 for 956 ns (20016 atoms). Deposited as NMRlipids Databank + simulation 340 and available from https://doi.org/10.5281/zenodo.1488094. sameAs: https://doi.org/10.5281/zenodo.1488094 datePublished: '2018-11-14' license: @@ -139,7 +143,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1488094 identifier: 10.5281/zenodo.1488094 url: https://doi.org/10.5281/zenodo.1488094 - name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS (various mixtures) with ECC-lipids force field, and Na+ (K+) counterions + name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS + (various mixtures) with ECC-lipids force field, and Na+ (K+) counterions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/38b/5ad/38b5ad22002bfa3c2a768098b9aa77cfca7bffa3/4ac8ab9e73138636924754f2e2f599bb88830137/README.yaml b/Simulations/38b/5ad/38b5ad22002bfa3c2a768098b9aa77cfca7bffa3/4ac8ab9e73138636924754f2e2f599bb88830137/README.yaml index 2d9769dcc9..437bfa6d01 100644 --- a/Simulations/38b/5ad/38b5ad22002bfa3c2a768098b9aa77cfca7bffa3/4ac8ab9e73138636924754f2e2f599bb88830137/README.yaml +++ b/Simulations/38b/5ad/38b5ad22002bfa3c2a768098b9aa77cfca7bffa3/4ac8ab9e73138636924754f2e2f599bb88830137/README.yaml @@ -54,9 +54,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 335 bioschema_properties: - name: Molecular dynamics trajectory of a POPE/POPG/SOD (60:20:20) bilayer at 310 K (Slipids, GROMACS 2018.3, 100 ns) [NMRlipids simulation 335] + name: Molecular dynamics trajectory of a POPE/POPG/SOD (60:20:20) bilayer at 310 + K (Slipids, GROMACS 2018.3, 100 ns) [NMRlipids simulation 335] alternateName: 126POPG_374POPE_25000SOL_126SOD_310K - description: Molecular dynamics trajectory of a lipid bilayer of 374 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 60 mol%), 126 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 20 mol%) and 126 SOD (20 mol%) at 310 K. Simulated with Slipids in GROMACS 2018.3 for 100 ns (137878 atoms). Deposited as NMRlipids Databank simulation 335 and available from https://doi.org/10.5281/zenodo.3238258. + description: Molecular dynamics trajectory of a lipid bilayer of 374 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, + 60 mol%), 126 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 20 mol%) + and 126 SOD (20 mol%) at 310 K. Simulated with Slipids in GROMACS 2018.3 for 100 + ns (137878 atoms). Deposited as NMRlipids Databank simulation 335 and available + from https://doi.org/10.5281/zenodo.3238258. sameAs: https://doi.org/10.5281/zenodo.3238258 datePublished: '2019-06-04' license: diff --git a/Simulations/38e/da7/38eda7ce056a265d6de16f6531d0ae2b12add606/38eda7ce056a265d6de16f6531d0ae2b12add606/README.yaml b/Simulations/38e/da7/38eda7ce056a265d6de16f6531d0ae2b12add606/38eda7ce056a265d6de16f6531d0ae2b12add606/README.yaml index 29f495f3a6..50cf97016d 100644 --- a/Simulations/38e/da7/38eda7ce056a265d6de16f6531d0ae2b12add606/38eda7ce056a265d6de16f6531d0ae2b12add606/README.yaml +++ b/Simulations/38e/da7/38eda7ce056a265d6de16f6531d0ae2b12add606/38eda7ce056a265d6de16f6531d0ae2b12add606/README.yaml @@ -47,9 +47,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 304 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (70:30) bilayer at 303 K (CHARMM36, OPENMM v7, 100 ns) [NMRlipids simulation 304] + name: Molecular dynamics trajectory of a POPC/CHOL (70:30) bilayer at 303 K (CHARMM36, + OPENMM v7, 100 ns) [NMRlipids simulation 304] alternateName: 84POPC_36CHOL_4800SOL_303K - description: Molecular dynamics trajectory of a lipid bilayer of 84 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 70 mol%) and 36 CHOL (cholesterol, 30 mol%) at 303 K. Simulated with CHARMM36 in OPENMM v7 for 100 ns (28320 atoms). Deposited as NMRlipids Databank simulation 304 and available from https://doi.org/10.5281/zenodo.163340. + description: Molecular dynamics trajectory of a lipid bilayer of 84 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 70 mol%) and 36 CHOL (cholesterol, 30 mol%) at 303 K. Simulated with CHARMM36 + in OPENMM v7 for 100 ns (28320 atoms). Deposited as NMRlipids Databank simulation + 304 and available from https://doi.org/10.5281/zenodo.163340. sameAs: https://doi.org/10.5281/zenodo.163340 datePublished: '2016-10-26' license: @@ -136,7 +140,9 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.163340 identifier: 10.5281/zenodo.163340 url: https://doi.org/10.5281/zenodo.163340 - name: Popc/Cholesterol (70:30) Lipid Membrane, 303K, Charmm36 Force Field Through The Use Of Gromacs Input Files, Simulation Files And 100 Ns Trajectory For Openmm Simulation Engine V7 + name: Popc/Cholesterol (70:30) Lipid Membrane, 303K, Charmm36 Force Field Through + The Use Of Gromacs Input Files, Simulation Files And 100 Ns Trajectory For Openmm + Simulation Engine V7 publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/391/ddf/391ddf2442a8699576d83b2ad8e80136dd6e8c9d/9f5bb844d10e44a75cd8d69d568117a1c8a39ec9/README.yaml b/Simulations/391/ddf/391ddf2442a8699576d83b2ad8e80136dd6e8c9d/9f5bb844d10e44a75cd8d69d568117a1c8a39ec9/README.yaml index cdf2ae10ac..b1fad33316 100644 --- a/Simulations/391/ddf/391ddf2442a8699576d83b2ad8e80136dd6e8c9d/9f5bb844d10e44a75cd8d69d568117a1c8a39ec9/README.yaml +++ b/Simulations/391/ddf/391ddf2442a8699576d83b2ad8e80136dd6e8c9d/9f5bb844d10e44a75cd8d69d568117a1c8a39ec9/README.yaml @@ -48,9 +48,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 508 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (57:21:21) bilayer at 298 K (MacRog, GROMACS 4.5, 50 ns) [NMRlipids simulation 508] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (57:21:21) bilayer at 298 + K (MacRog, GROMACS 4.5, 50 ns) [NMRlipids simulation 508] alternateName: 288POPC_14392SOL_108SOD_108CLA_298K - description: Molecular dynamics trajectory of a lipid bilayer of 288 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 57 mol%), 108 CLA (21 mol%) and 108 SOD (21 mol%) at 298 K. Simulated with MacRog in GROMACS 4.5 for 50 ns (81984 atoms). Deposited as NMRlipids Databank simulation 508 and available from https://doi.org/10.5281/zenodo.14976. + description: Molecular dynamics trajectory of a lipid bilayer of 288 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 57 mol%), 108 CLA (21 mol%) and 108 SOD (21 mol%) at 298 K. Simulated with MacRog + in GROMACS 4.5 for 50 ns (81984 atoms). Deposited as NMRlipids Databank simulation + 508 and available from https://doi.org/10.5281/zenodo.14976. sameAs: https://doi.org/10.5281/zenodo.14976 datePublished: '2015-02-10' license: diff --git a/Simulations/393/0bc/3930bc1addae9455c0c46e225fedbe7ed1db93ad/c1c23bdd2acb5f21f947cad163ba8274a0edf41d/README.yaml b/Simulations/393/0bc/3930bc1addae9455c0c46e225fedbe7ed1db93ad/c1c23bdd2acb5f21f947cad163ba8274a0edf41d/README.yaml index 63e29681f1..1e2afcc2f3 100644 --- a/Simulations/393/0bc/3930bc1addae9455c0c46e225fedbe7ed1db93ad/c1c23bdd2acb5f21f947cad163ba8274a0edf41d/README.yaml +++ b/Simulations/393/0bc/3930bc1addae9455c0c46e225fedbe7ed1db93ad/c1c23bdd2acb5f21f947cad163ba8274a0edf41d/README.yaml @@ -58,9 +58,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 322 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPG/SOD (54:23:23) bilayer at 310 K (GROMOS-CKP, GROMACS 2018.3, 100 ns) [NMRlipids simulation 322] + name: Molecular dynamics trajectory of a POPC/POPG/SOD (54:23:23) bilayer at 310 + K (GROMOS-CKP, GROMACS 2018.3, 100 ns) [NMRlipids simulation 322] alternateName: 350POPC_150POPG_25000SOL_150SOD_310K - description: Molecular dynamics trajectory of a lipid bilayer of 350 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 54 mol%), 150 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 23 mol%) and 150 SOD (23 mol%) at 310 K. Simulated with GROMOS-CKP in GROMACS 2018.3 for 100 ns (101300 atoms). Deposited as NMRlipids Databank simulation 322 and available from https://doi.org/10.5281/zenodo.3266240. + description: Molecular dynamics trajectory of a lipid bilayer of 350 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 54 mol%), 150 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 23 mol%) + and 150 SOD (23 mol%) at 310 K. Simulated with GROMOS-CKP in GROMACS 2018.3 for + 100 ns (101300 atoms). Deposited as NMRlipids Databank simulation 322 and available + from https://doi.org/10.5281/zenodo.3266240. sameAs: https://doi.org/10.5281/zenodo.3266240 datePublished: '2019-07-02' license: diff --git a/Simulations/39b/eb6/39beb6ec9a40f78b9aaad0188ea679cdeeb83078/951177f7e152b408149e2ec4e16d660bccc94563/README.yaml b/Simulations/39b/eb6/39beb6ec9a40f78b9aaad0188ea679cdeeb83078/951177f7e152b408149e2ec4e16d660bccc94563/README.yaml index 8a4cddebb2..4bdb1ef04f 100644 --- a/Simulations/39b/eb6/39beb6ec9a40f78b9aaad0188ea679cdeeb83078/951177f7e152b408149e2ec4e16d660bccc94563/README.yaml +++ b/Simulations/39b/eb6/39beb6ec9a40f78b9aaad0188ea679cdeeb83078/951177f7e152b408149e2ec4e16d660bccc94563/README.yaml @@ -41,9 +41,12 @@ SOFTWARE: gromacs DIR_WRK: /usr/home/bort/Databank ID: 376 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 303 K (Slipids, GROMACS 2020.1, 1200 ns) [NMRlipids simulation 376] + name: Molecular dynamics trajectory of a POPC bilayer at 303 K (Slipids, GROMACS + 2020.1, 1200 ns) [NMRlipids simulation 376] alternateName: 122POPC_4880SOL_303K - description: Molecular dynamics trajectory of a lipid bilayer of 122 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 303 K. Simulated with Slipids in GROMACS 2020.1 for 1200 ns (30988 atoms). Deposited as NMRlipids Databank simulation 376 and available from https://doi.org/10.5281/zenodo.4352287. + description: Molecular dynamics trajectory of a lipid bilayer of 122 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 303 K. Simulated with Slipids in GROMACS 2020.1 for 1200 ns (30988 atoms). + Deposited as NMRlipids Databank simulation 376 and available from https://doi.org/10.5281/zenodo.4352287. sameAs: https://doi.org/10.5281/zenodo.4352287 datePublished: '2020-12-18' license: diff --git a/Simulations/39e/0a0/39e0a046fb51a708a307b1b773e8c81d7630cfe3/9fd3575b9633a4c51c890e1bfc7aff5303ac7f95/README.yaml b/Simulations/39e/0a0/39e0a046fb51a708a307b1b773e8c81d7630cfe3/9fd3575b9633a4c51c890e1bfc7aff5303ac7f95/README.yaml index ff16f35dc0..b987518604 100644 --- a/Simulations/39e/0a0/39e0a046fb51a708a307b1b773e8c81d7630cfe3/9fd3575b9633a4c51c890e1bfc7aff5303ac7f95/README.yaml +++ b/Simulations/39e/0a0/39e0a046fb51a708a307b1b773e8c81d7630cfe3/9fd3575b9633a4c51c890e1bfc7aff5303ac7f95/README.yaml @@ -52,9 +52,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 576 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (92:4:4) bilayer at 310 K (CHARMM36 noNBFIX, GROMACS, 239 ns) [NMRlipids simulation 576] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (92:4:4) bilayer at 310 K + (CHARMM36 noNBFIX, GROMACS, 239 ns) [NMRlipids simulation 576] alternateName: 200POPC_9000SOL_9SOD_18CLA_310K_noNBFIX - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 92 mol%), 9 CLA (4 mol%) and 9 SOD (4 mol%) at 310 K. Simulated with CHARMM36 noNBFIX in GROMACS for 239 ns (53818 atoms). Deposited as NMRlipids Databank simulation 576 and available from https://doi.org/10.5281/zenodo.3434396. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 92 mol%), 9 CLA (4 mol%) and 9 SOD (4 mol%) at 310 K. Simulated with CHARMM36 + noNBFIX in GROMACS for 239 ns (53818 atoms). Deposited as NMRlipids Databank simulation + 576 and available from https://doi.org/10.5281/zenodo.3434396. sameAs: https://doi.org/10.5281/zenodo.3434396 datePublished: '2019-09-17' license: diff --git a/Simulations/39f/484/39f484fbfc281cd29a27c47cdb99366ebb62b9ab/8273b9817a77d63451f6ead358e2a458eb83149e/README.yaml b/Simulations/39f/484/39f484fbfc281cd29a27c47cdb99366ebb62b9ab/8273b9817a77d63451f6ead358e2a458eb83149e/README.yaml index e3766cc22a..3b467aa145 100644 --- a/Simulations/39f/484/39f484fbfc281cd29a27c47cdb99366ebb62b9ab/8273b9817a77d63451f6ead358e2a458eb83149e/README.yaml +++ b/Simulations/39f/484/39f484fbfc281cd29a27c47cdb99366ebb62b9ab/8273b9817a77d63451f6ead358e2a458eb83149e/README.yaml @@ -44,9 +44,12 @@ EXPERIMENT: SOPC: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a SOPC bilayer at 333.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 630] + name: Molecular dynamics trajectory of a SOPC bilayer at 333.15 K (CHARMM36, GROMACS, + 1001 ns) [NMRlipids simulation 630] alternateName: 64SOPC_3200SOL_333K - description: Molecular dynamics trajectory of a lipid bilayer of 64 SOPC (1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (18560 atoms). Deposited as NMRlipids Databank simulation 630 and available from https://doi.org/10.5281/zenodo.6943413. + description: Molecular dynamics trajectory of a lipid bilayer of 64 SOPC (1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (18560 atoms). Deposited + as NMRlipids Databank simulation 630 and available from https://doi.org/10.5281/zenodo.6943413. sameAs: https://doi.org/10.5281/zenodo.6943413 datePublished: '2022-07-30' license: @@ -134,7 +137,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.6943413 identifier: 10.5281/zenodo.6943413 url: https://doi.org/10.5281/zenodo.6943413 - name: Simulations of different single-component bilayers, three different system sizes + name: Simulations of different single-component bilayers, three different system + sizes publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/3a2/6a9/3a26a9b5cce79fce362a17e30b4a74e2b2ee8d71/3a26a9b5cce79fce362a17e30b4a74e2b2ee8d71/README.yaml b/Simulations/3a2/6a9/3a26a9b5cce79fce362a17e30b4a74e2b2ee8d71/3a26a9b5cce79fce362a17e30b4a74e2b2ee8d71/README.yaml index d7dbbc0bb1..e33f505d0b 100644 --- a/Simulations/3a2/6a9/3a26a9b5cce79fce362a17e30b4a74e2b2ee8d71/3a26a9b5cce79fce362a17e30b4a74e2b2ee8d71/README.yaml +++ b/Simulations/3a2/6a9/3a26a9b5cce79fce362a17e30b4a74e2b2ee8d71/3a26a9b5cce79fce362a17e30b4a74e2b2ee8d71/README.yaml @@ -49,9 +49,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 168 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (70:30) bilayer at 303 K (CHARMM36, OPENMM v7, 100 ns) [NMRlipids simulation 168] + name: Molecular dynamics trajectory of a POPC/CHOL (70:30) bilayer at 303 K (CHARMM36, + OPENMM v7, 100 ns) [NMRlipids simulation 168] alternateName: 84POPC_36CHOL_4800SOL_303K - description: Molecular dynamics trajectory of a lipid bilayer of 84 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 70 mol%) and 36 CHOL (cholesterol, 30 mol%) at 303 K. Simulated with CHARMM36 in OPENMM v7 for 100 ns (28320 atoms). Deposited as NMRlipids Databank simulation 168 and available from https://doi.org/10.5281/zenodo.163333. + description: Molecular dynamics trajectory of a lipid bilayer of 84 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 70 mol%) and 36 CHOL (cholesterol, 30 mol%) at 303 K. Simulated with CHARMM36 + in OPENMM v7 for 100 ns (28320 atoms). Deposited as NMRlipids Databank simulation + 168 and available from https://doi.org/10.5281/zenodo.163333. sameAs: https://doi.org/10.5281/zenodo.163333 datePublished: '2016-10-26' license: @@ -138,7 +142,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.163333 identifier: 10.5281/zenodo.163333 url: https://doi.org/10.5281/zenodo.163333 - name: Popc/Cholesterol (70:30) Lipid Membrane, 303K, Charmm36 Force Field, Simulation Files And 100 Ns Trajectory For Openmm Simulation Engine V7 + name: Popc/Cholesterol (70:30) Lipid Membrane, 303K, Charmm36 Force Field, Simulation + Files And 100 Ns Trajectory For Openmm Simulation Engine V7 publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/3ae/2ad/3ae2ad254c7748843eebd62365d21cdc7712b519/0a3d4c6d2fceb62705ed272b2f4aa607477b4337/README.yaml b/Simulations/3ae/2ad/3ae2ad254c7748843eebd62365d21cdc7712b519/0a3d4c6d2fceb62705ed272b2f4aa607477b4337/README.yaml index 76681889e7..f36a5c5e3a 100644 --- a/Simulations/3ae/2ad/3ae2ad254c7748843eebd62365d21cdc7712b519/0a3d4c6d2fceb62705ed272b2f4aa607477b4337/README.yaml +++ b/Simulations/3ae/2ad/3ae2ad254c7748843eebd62365d21cdc7712b519/0a3d4c6d2fceb62705ed272b2f4aa607477b4337/README.yaml @@ -45,9 +45,12 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/1 ID: 664 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 298.15 K (Slipids, GROMACS 2021, 1001 ns) [NMRlipids simulation 664] + name: Molecular dynamics trajectory of a POPC bilayer at 298.15 K (Slipids, GROMACS + 2021, 1001 ns) [NMRlipids simulation 664] alternateName: Slipids_POPC_S - description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 298.15 K. Simulated with Slipids in GROMACS 2021 for 1001 ns (18176 atoms). Deposited as NMRlipids Databank simulation 664 and available from https://doi.org/10.5281/zenodo.7022749. + description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 298.15 K. Simulated with Slipids in GROMACS 2021 for 1001 ns (18176 atoms). + Deposited as NMRlipids Databank simulation 664 and available from https://doi.org/10.5281/zenodo.7022749. sameAs: https://doi.org/10.5281/zenodo.7022749 datePublished: '2022-08-23' license: diff --git a/Simulations/3b7/495/3b7495748b4ce4ff1283bf78594bfabe40c19f21/e08d9a47fccf7182de0582efa99e1d9909acaee6/README.yaml b/Simulations/3b7/495/3b7495748b4ce4ff1283bf78594bfabe40c19f21/e08d9a47fccf7182de0582efa99e1d9909acaee6/README.yaml index 776dac9651..1c8ee1dd1f 100644 --- a/Simulations/3b7/495/3b7495748b4ce4ff1283bf78594bfabe40c19f21/e08d9a47fccf7182de0582efa99e1d9909acaee6/README.yaml +++ b/Simulations/3b7/495/3b7495748b4ce4ff1283bf78594bfabe40c19f21/e08d9a47fccf7182de0582efa99e1d9909acaee6/README.yaml @@ -55,9 +55,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 867 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/NH4/POPI (67:17:17) bilayer at 310 K (CHARMM36, GROMACS 2022.4, 500 ns) [NMRlipids simulation 867] + name: Molecular dynamics trajectory of a POPC/NH4/POPI (67:17:17) bilayer at 310 + K (CHARMM36, GROMACS 2022.4, 500 ns) [NMRlipids simulation 867] alternateName: POPI-POPC (20:80), full hydration, 310 K, NH4+ counter ions - description: Molecular dynamics trajectory of a lipid bilayer of 160 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 67 mol%), 40 NH4 (17 mol%) and 40 POPI (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoinositol, 17 mol%) at 310 K. Simulated with CHARMM36 in GROMACS 2022.4 for 500 ns (57120 atoms). Deposited as NMRlipids Databank simulation 867 and available from https://doi.org/10.5281/zenodo.10259002. + description: Molecular dynamics trajectory of a lipid bilayer of 160 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 67 mol%), 40 NH4 (17 mol%) and 40 POPI (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoinositol, + 17 mol%) at 310 K. Simulated with CHARMM36 in GROMACS 2022.4 for 500 ns (57120 + atoms). Deposited as NMRlipids Databank simulation 867 and available from https://doi.org/10.5281/zenodo.10259002. sameAs: https://doi.org/10.5281/zenodo.10259002 datePublished: '2023-12-18' license: diff --git a/Simulations/3bc/a62/3bca622bc5c892872cbb62eda208e4d43a98a320/e45c78f0d726cea8c0966870f562f5a0ae896885/README.yaml b/Simulations/3bc/a62/3bca622bc5c892872cbb62eda208e4d43a98a320/e45c78f0d726cea8c0966870f562f5a0ae896885/README.yaml index 067faed6ca..084ae46604 100644 --- a/Simulations/3bc/a62/3bca622bc5c892872cbb62eda208e4d43a98a320/e45c78f0d726cea8c0966870f562f5a0ae896885/README.yaml +++ b/Simulations/3bc/a62/3bca622bc5c892872cbb62eda208e4d43a98a320/e45c78f0d726cea8c0966870f562f5a0ae896885/README.yaml @@ -44,9 +44,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 330 bioschema_properties: - name: Molecular dynamics trajectory of a DOPC bilayer at 300 K (Berger, GROMACS, 300 ns) [NMRlipids simulation 330] + name: Molecular dynamics trajectory of a DOPC bilayer at 300 K (Berger, GROMACS, + 300 ns) [NMRlipids simulation 330] alternateName: 256DOPC_11096SOL_300K_Berger - description: Molecular dynamics trajectory of a lipid bilayer of 256 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) at 300 K. Simulated with Berger in GROMACS for 300 ns (47112 atoms). Deposited as NMRlipids Databank simulation 330 and available from https://doi.org/10.5281/zenodo.1402411. + description: Molecular dynamics trajectory of a lipid bilayer of 256 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) + at 300 K. Simulated with Berger in GROMACS for 300 ns (47112 atoms). Deposited + as NMRlipids Databank simulation 330 and available from https://doi.org/10.5281/zenodo.1402411. sameAs: https://doi.org/10.5281/zenodo.1402411 datePublished: '2018-08-23' license: diff --git a/Simulations/3bc/fec/3bcfec940cb844905331c500649f8163e739f3e6/018b3585ccf055e9087a4b50ce06a3d9e4515fcb/README.yaml b/Simulations/3bc/fec/3bcfec940cb844905331c500649f8163e739f3e6/018b3585ccf055e9087a4b50ce06a3d9e4515fcb/README.yaml index cdfd1cf1dd..c1d9e9f458 100644 --- a/Simulations/3bc/fec/3bcfec940cb844905331c500649f8163e739f3e6/018b3585ccf055e9087a4b50ce06a3d9e4515fcb/README.yaml +++ b/Simulations/3bc/fec/3bcfec940cb844905331c500649f8163e739f3e6/018b3585ccf055e9087a4b50ce06a3d9e4515fcb/README.yaml @@ -49,9 +49,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 329 bioschema_properties: - name: Molecular dynamics trajectory of a DOPS/SOD (50:50) bilayer at 303 K (Berger, GROMACS, 100 ns) [NMRlipids simulation 329] + name: Molecular dynamics trajectory of a DOPS/SOD (50:50) bilayer at 303 K (Berger, + GROMACS, 100 ns) [NMRlipids simulation 329] alternateName: 128DOPS_4480SOL_128SOD_303K_v2 - description: Molecular dynamics trajectory of a lipid bilayer of 128 DOPS (1,2-dioleoyl-sn-glycero-3-phospho-L-serine, 50 mol%) and 128 SOD (50 mol%) at 303 K. Simulated with Berger in GROMACS for 100 ns (20864 atoms). Deposited as NMRlipids Databank simulation 329 and available from https://doi.org/10.5281/zenodo.1129419. + description: Molecular dynamics trajectory of a lipid bilayer of 128 DOPS (1,2-dioleoyl-sn-glycero-3-phospho-L-serine, + 50 mol%) and 128 SOD (50 mol%) at 303 K. Simulated with Berger in GROMACS for + 100 ns (20864 atoms). Deposited as NMRlipids Databank simulation 329 and available + from https://doi.org/10.5281/zenodo.1129419. sameAs: https://doi.org/10.5281/zenodo.1129419 datePublished: '2017-12-24' license: diff --git a/Simulations/3c4/732/3c473214491fd52562860b55efb5ef4f1f97bf16/e4dcad684cadd45b6c398eabbe39329dbb6b12bb/README.yaml b/Simulations/3c4/732/3c473214491fd52562860b55efb5ef4f1f97bf16/e4dcad684cadd45b6c398eabbe39329dbb6b12bb/README.yaml index 4254cf31ed..578c3be990 100644 --- a/Simulations/3c4/732/3c473214491fd52562860b55efb5ef4f1f97bf16/e4dcad684cadd45b6c398eabbe39329dbb6b12bb/README.yaml +++ b/Simulations/3c4/732/3c473214491fd52562860b55efb5ef4f1f97bf16/e4dcad684cadd45b6c398eabbe39329dbb6b12bb/README.yaml @@ -53,9 +53,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/8 ID: 275 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (62:38) bilayer at 298.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 275] + name: Molecular dynamics trajectory of a POPC/CHOL (62:38) bilayer at 298.15 K (CHARMM36, + GROMACS, 1001 ns) [NMRlipids simulation 275] alternateName: 256POPC_160CHOL_20800SOL_298K - description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 62 mol%) and 160 CHOL (cholesterol, 38 mol%) at 298.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (108544 atoms). Deposited as NMRlipids Databank simulation 275 and available from https://doi.org/10.5281/zenodo.5767451. + description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 62 mol%) and 160 CHOL (cholesterol, 38 mol%) at 298.15 K. Simulated with CHARMM36 + in GROMACS for 1001 ns (108544 atoms). Deposited as NMRlipids Databank simulation + 275 and available from https://doi.org/10.5281/zenodo.5767451. sameAs: https://doi.org/10.5281/zenodo.5767451 datePublished: '2021-12-08' license: diff --git a/Simulations/3cd/a05/3cda05f38c674e5011880144acbef0b3b4b1c449/ba4e53592af3891ca6bb0bfb7ec2e1da0c559243/README.yaml b/Simulations/3cd/a05/3cda05f38c674e5011880144acbef0b3b4b1c449/ba4e53592af3891ca6bb0bfb7ec2e1da0c559243/README.yaml index 76b37529bb..4559269014 100644 --- a/Simulations/3cd/a05/3cda05f38c674e5011880144acbef0b3b4b1c449/ba4e53592af3891ca6bb0bfb7ec2e1da0c559243/README.yaml +++ b/Simulations/3cd/a05/3cda05f38c674e5011880144acbef0b3b4b1c449/ba4e53592af3891ca6bb0bfb7ec2e1da0c559243/README.yaml @@ -54,9 +54,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 117 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/DHMDMAB (42:29:29) bilayer at 313 K (Lipid14, GROMACS, 180 ns) [NMRlipids simulation 117] + name: Molecular dynamics trajectory of a POPC/CLA/DHMDMAB (42:29:29) bilayer at + 313 K (Lipid14, GROMACS, 180 ns) [NMRlipids simulation 117] alternateName: 100POPC_70DHMDMAB_6214SOL_50CLA_313K - description: Molecular dynamics trajectory of a lipid bilayer of 100 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 42 mol%), 70 CLA (29 mol%) and 70 DHMDMAB (dihexadecyldimethylammonium, 29 mol%) at 313 K. Simulated with Lipid14 in GROMACS for 180 ns (39602 atoms). Deposited as NMRlipids Databank simulation 117 and available from https://doi.org/10.5281/zenodo.1020671. + description: Molecular dynamics trajectory of a lipid bilayer of 100 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 42 mol%), 70 CLA (29 mol%) and 70 DHMDMAB (dihexadecyldimethylammonium, 29 mol%) + at 313 K. Simulated with Lipid14 in GROMACS for 180 ns (39602 atoms). Deposited + as NMRlipids Databank simulation 117 and available from https://doi.org/10.5281/zenodo.1020671. sameAs: https://doi.org/10.5281/zenodo.1020671 datePublished: '2017-10-18' license: @@ -145,7 +149,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1020671 identifier: 10.5281/zenodo.1020671 url: https://doi.org/10.5281/zenodo.1020671 - name: Popc Bilayer With 42% Of Dihexadecyldimethylammonium Simulated At T313K With The Lipid14 Model Using Gromacs + name: Popc Bilayer With 42% Of Dihexadecyldimethylammonium Simulated At T313K + With The Lipid14 Model Using Gromacs publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/3cd/dd2/3cddd2c3251384a2cde3c0fad37e15db8570a6a6/ed4bf98a37c37c12573886bcadbc1320382bd154/README.yaml b/Simulations/3cd/dd2/3cddd2c3251384a2cde3c0fad37e15db8570a6a6/ed4bf98a37c37c12573886bcadbc1320382bd154/README.yaml index edffc7d522..843c80cece 100644 --- a/Simulations/3cd/dd2/3cddd2c3251384a2cde3c0fad37e15db8570a6a6/ed4bf98a37c37c12573886bcadbc1320382bd154/README.yaml +++ b/Simulations/3cd/dd2/3cddd2c3251384a2cde3c0fad37e15db8570a6a6/ed4bf98a37c37c12573886bcadbc1320382bd154/README.yaml @@ -44,9 +44,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 817 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 300 K (OPLS4, GROMACS Desmond 2022-2, 650 ns) [NMRlipids simulation 817] + name: Molecular dynamics trajectory of a POPC bilayer at 300 K (OPLS4, GROMACS Desmond + 2022-2, 650 ns) [NMRlipids simulation 817] alternateName: 200POPC_1kSOL_300K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 300 K. Simulated with OPLS4 in GROMACS Desmond 2022-2 for 650 ns (29800 atoms). Deposited as NMRlipids Databank simulation 817 and available from https://doi.org/10.5281/zenodo.10949612. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 300 K. Simulated with OPLS4 in GROMACS Desmond 2022-2 for 650 ns (29800 atoms). + Deposited as NMRlipids Databank simulation 817 and available from https://doi.org/10.5281/zenodo.10949612. sameAs: https://doi.org/10.5281/zenodo.10949612 datePublished: '2024-04-09' license: diff --git a/Simulations/3d1/f82/3d1f825918b4a3fd2f2dc52ad9d6948a78773bd0/e269c2c27722ad263b0d0f883e62e28f60d1ed1a/README.yaml b/Simulations/3d1/f82/3d1f825918b4a3fd2f2dc52ad9d6948a78773bd0/e269c2c27722ad263b0d0f883e62e28f60d1ed1a/README.yaml index 25f7bece7d..8a1f3f7e4b 100644 --- a/Simulations/3d1/f82/3d1f825918b4a3fd2f2dc52ad9d6948a78773bd0/e269c2c27722ad263b0d0f883e62e28f60d1ed1a/README.yaml +++ b/Simulations/3d1/f82/3d1f825918b4a3fd2f2dc52ad9d6948a78773bd0/e269c2c27722ad263b0d0f883e62e28f60d1ed1a/README.yaml @@ -57,9 +57,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 399 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL/CLA/SOD (76:8:8:8) bilayer at 310 K (Slipids with ECC-scaled ions (Kohagen), GROMACS 4.6, 200 ns) [NMRlipids simulation 399] + name: Molecular dynamics trajectory of a POPC/CHOL/CLA/SOD (76:8:8:8) bilayer at + 310 K (Slipids with ECC-scaled ions (Kohagen), GROMACS 4.6, 200 ns) [NMRlipids + simulation 399] alternateName: 22CHOL_200POPC_9000SOL_21SOD_21CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 76 mol%), 22 CHOL (cholesterol, 8 mol%), 21 CLA (8 mol%) and 21 SOD (8 mol%) at 310 K. Simulated with Slipids with ECC-scaled ions (Kohagen) in GROMACS 4.6 for 200 ns (55470 atoms). Deposited as NMRlipids Databank simulation 399 and available from https://doi.org/10.5281/zenodo.259343. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 76 mol%), 22 CHOL (cholesterol, 8 mol%), 21 CLA (8 mol%) and 21 SOD (8 mol%) at + 310 K. Simulated with Slipids with ECC-scaled ions (Kohagen) in GROMACS 4.6 for + 200 ns (55470 atoms). Deposited as NMRlipids Databank simulation 399 and available + from https://doi.org/10.5281/zenodo.259343. sameAs: https://doi.org/10.5281/zenodo.259343 datePublished: '2017-01-24' license: @@ -149,7 +155,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.259343 identifier: 10.5281/zenodo.259343 url: https://doi.org/10.5281/zenodo.259343 - name: Popc With Varying Amounts Of Cholesterol, 130 Mm Of Nacl. Slipids With Ecc-Scaled Ions + name: Popc With Varying Amounts Of Cholesterol, 130 Mm Of Nacl. Slipids With Ecc-Scaled + Ions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/3da/77f/3da77f2fd11552f0b871d5b83133838d3251aa5a/3da77f2fd11552f0b871d5b83133838d3251aa5a/README.yaml b/Simulations/3da/77f/3da77f2fd11552f0b871d5b83133838d3251aa5a/3da77f2fd11552f0b871d5b83133838d3251aa5a/README.yaml index 18cfeb7997..ef74d331a6 100644 --- a/Simulations/3da/77f/3da77f2fd11552f0b871d5b83133838d3251aa5a/3da77f2fd11552f0b871d5b83133838d3251aa5a/README.yaml +++ b/Simulations/3da/77f/3da77f2fd11552f0b871d5b83133838d3251aa5a/3da77f2fd11552f0b871d5b83133838d3251aa5a/README.yaml @@ -38,9 +38,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 743 bioschema_properties: - name: Molecular dynamics trajectory of a POPE bilayer at 303 K (Charmm-Drude, OPENMM 7.5.0, 300 ns) [NMRlipids simulation 743] + name: Molecular dynamics trajectory of a POPE bilayer at 303 K (Charmm-Drude, OPENMM + 7.5.0, 300 ns) [NMRlipids simulation 743] alternateName: 72POPE_5040SOL_303K - description: Molecular dynamics trajectory of a lipid bilayer of 144 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) at 303 K. Simulated with Charmm-Drude in OPENMM 7.5.0 for 300 ns (51408 atoms). Deposited as NMRlipids Databank simulation 743 and available from https://doi.org/10.5281/zenodo.7604627. + description: Molecular dynamics trajectory of a lipid bilayer of 144 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) + at 303 K. Simulated with Charmm-Drude in OPENMM 7.5.0 for 300 ns (51408 atoms). + Deposited as NMRlipids Databank simulation 743 and available from https://doi.org/10.5281/zenodo.7604627. sameAs: https://doi.org/10.5281/zenodo.7604627 datePublished: '2021-04-06' license: @@ -129,7 +132,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.7604627 identifier: 10.5281/zenodo.7604627 url: https://doi.org/10.5281/zenodo.7604627 - name: Pure POPE membrane simulations with the CHARMM-Drude force field (OpenMM 7.5.0) + name: Pure POPE membrane simulations with the CHARMM-Drude force field (OpenMM + 7.5.0) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/3eb/0d7/3eb0d73b617d7d221e13ef92ca6c515e8ef8dbfb/1b2aabd7319581577cc149d9b44a6e14424e316d/README.yaml b/Simulations/3eb/0d7/3eb0d73b617d7d221e13ef92ca6c515e8ef8dbfb/1b2aabd7319581577cc149d9b44a6e14424e316d/README.yaml index b411b9052f..bcd6e57fda 100644 --- a/Simulations/3eb/0d7/3eb0d73b617d7d221e13ef92ca6c515e8ef8dbfb/1b2aabd7319581577cc149d9b44a6e14424e316d/README.yaml +++ b/Simulations/3eb/0d7/3eb0d73b617d7d221e13ef92ca6c515e8ef8dbfb/1b2aabd7319581577cc149d9b44a6e14424e316d/README.yaml @@ -43,9 +43,12 @@ WARNINGS: PBC: z-jumps ID: 150 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 303 K (CHARMM36, GROMACS 4.5, 40 ns) [NMRlipids simulation 150] + name: Molecular dynamics trajectory of a POPC bilayer at 303 K (CHARMM36, GROMACS + 4.5, 40 ns) [NMRlipids simulation 150] alternateName: 72POPC_1080SOL_303K - description: Molecular dynamics trajectory of a lipid bilayer of 72 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 303 K. Simulated with CHARMM36 in GROMACS 4.5 for 40 ns (12888 atoms). Deposited as NMRlipids Databank simulation 150 and available from https://doi.org/10.5281/zenodo.4740115. + description: Molecular dynamics trajectory of a lipid bilayer of 72 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 303 K. Simulated with CHARMM36 in GROMACS 4.5 for 40 ns (12888 atoms). Deposited + as NMRlipids Databank simulation 150 and available from https://doi.org/10.5281/zenodo.4740115. sameAs: https://doi.org/10.5281/zenodo.4740115 datePublished: '2015-01-14' license: @@ -132,7 +135,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.4740115 identifier: 10.5281/zenodo.4740115 url: https://doi.org/10.5281/zenodo.4740115 - name: MD simulation trajectory and related files for POPC bilayer in medium low hydration (CHARMM36, Gromacs 4.5) + name: MD simulation trajectory and related files for POPC bilayer in medium low + hydration (CHARMM36, Gromacs 4.5) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/3ed/c37/3edc37b849c9f8e3c4787450ab4cf57fa9eaadf4/cc41982e8e55785a46a668f0f5a943cb7db5329c/README.yaml b/Simulations/3ed/c37/3edc37b849c9f8e3c4787450ab4cf57fa9eaadf4/cc41982e8e55785a46a668f0f5a943cb7db5329c/README.yaml index 2e5b58b6d4..7a9d22d18e 100644 --- a/Simulations/3ed/c37/3edc37b849c9f8e3c4787450ab4cf57fa9eaadf4/cc41982e8e55785a46a668f0f5a943cb7db5329c/README.yaml +++ b/Simulations/3ed/c37/3edc37b849c9f8e3c4787450ab4cf57fa9eaadf4/cc41982e8e55785a46a668f0f5a943cb7db5329c/README.yaml @@ -56,9 +56,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 208 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD/CHOL (37:30:30:4) bilayer at 310 K (Slipids with ions by Smith & Dang, GROMACS 4.6, 200 ns) [NMRlipids simulation 208] + name: Molecular dynamics trajectory of a POPC/CLA/SOD/CHOL (37:30:30:4) bilayer + at 310 K (Slipids with ions by Smith & Dang, GROMACS 4.6, 200 ns) [NMRlipids simulation + 208] alternateName: 22CHOL_200POPC_9000SOL_162SOD_162CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 37 mol%), 162 CLA (30 mol%), 162 SOD (30 mol%) and 22 CHOL (cholesterol, 4 mol%) at 310 K. Simulated with Slipids with ions by Smith & Dang in GROMACS 4.6 for 200 ns (55752 atoms). Deposited as NMRlipids Databank simulation 208 and available from https://doi.org/10.5281/zenodo.259341. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 37 mol%), 162 CLA (30 mol%), 162 SOD (30 mol%) and 22 CHOL (cholesterol, 4 mol%) + at 310 K. Simulated with Slipids with ions by Smith & Dang in GROMACS 4.6 for + 200 ns (55752 atoms). Deposited as NMRlipids Databank simulation 208 and available + from https://doi.org/10.5281/zenodo.259341. sameAs: https://doi.org/10.5281/zenodo.259341 datePublished: '2017-01-24' license: @@ -148,7 +154,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.259341 identifier: 10.5281/zenodo.259341 url: https://doi.org/10.5281/zenodo.259341 - name: Popc With Varying Amounts Of Cholesterol, 1 M Of Nacl. Slipids With Ions By Smith & Dang + name: Popc With Varying Amounts Of Cholesterol, 1 M Of Nacl. Slipids With Ions + By Smith & Dang publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/3ef/72b/3ef72bbbb9a3071dd6dcf9daf45375dd0561e4d4/1fe82655b1eb044705ade4ac9bfe85699ebbc904/README.yaml b/Simulations/3ef/72b/3ef72bbbb9a3071dd6dcf9daf45375dd0561e4d4/1fe82655b1eb044705ade4ac9bfe85699ebbc904/README.yaml index db890956cd..077ee37d80 100644 --- a/Simulations/3ef/72b/3ef72bbbb9a3071dd6dcf9daf45375dd0561e4d4/1fe82655b1eb044705ade4ac9bfe85699ebbc904/README.yaml +++ b/Simulations/3ef/72b/3ef72bbbb9a3071dd6dcf9daf45375dd0561e4d4/1fe82655b1eb044705ade4ac9bfe85699ebbc904/README.yaml @@ -45,9 +45,12 @@ EXPERIMENT: - 10.1016/j.bbamem.2011.07.022/11 ID: 595 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 313 K (ECC-lipids, GROMACS 5.1.4, 300 ns) [NMRlipids simulation 595] + name: Molecular dynamics trajectory of a POPC bilayer at 313 K (ECC-lipids, GROMACS + 5.1.4, 300 ns) [NMRlipids simulation 595] alternateName: 128POPC_6400SOL_313K_TIP3p-FBmodel - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 300 ns (36352 atoms). Deposited as NMRlipids Databank simulation 595 and available from https://doi.org/10.5281/zenodo.1118980. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 300 ns (36352 atoms). + Deposited as NMRlipids Databank simulation 595 and available from https://doi.org/10.5281/zenodo.1118980. sameAs: https://doi.org/10.5281/zenodo.1118980 datePublished: '2017-12-19' license: @@ -136,7 +139,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1118980 identifier: 10.5281/zenodo.1118980 url: https://doi.org/10.5281/zenodo.1118980 - name: Simulations Of Popc Lipid Bilayer In Water Solution At Various Nacl And Cacl2 Concentrations Using Ecc-Popc Force Field And Various Water Models + name: Simulations Of Popc Lipid Bilayer In Water Solution At Various Nacl And + Cacl2 Concentrations Using Ecc-Popc Force Field And Various Water Models publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/3f1/b7a/3f1b7ab8e9302ee3e990c900fd32011eed19ca39/dee95a62107c64f37914a28b0156dad4cfb5863d/README.yaml b/Simulations/3f1/b7a/3f1b7ab8e9302ee3e990c900fd32011eed19ca39/dee95a62107c64f37914a28b0156dad4cfb5863d/README.yaml index bfc443d27c..72a91fbbe1 100644 --- a/Simulations/3f1/b7a/3f1b7ab8e9302ee3e990c900fd32011eed19ca39/dee95a62107c64f37914a28b0156dad4cfb5863d/README.yaml +++ b/Simulations/3f1/b7a/3f1b7ab8e9302ee3e990c900fd32011eed19ca39/dee95a62107c64f37914a28b0156dad4cfb5863d/README.yaml @@ -58,9 +58,15 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 252 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CHOL/CAL (40:29:17:14) bilayer at 310.15 K (CHARMM36 with incorrect multiplicity in dihedrals and ECC ions, GROMACS 5.0, 800 ns) [NMRlipids simulation 252] + name: Molecular dynamics trajectory of a POPC/CLA/CHOL/CAL (40:29:17:14) bilayer + at 310.15 K (CHARMM36 with incorrect multiplicity in dihedrals and ECC ions, GROMACS + 5.0, 800 ns) [NMRlipids simulation 252] alternateName: 86CHOL_200POPC_9000SOL_73CAL_146CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 40 mol%), 146 CLA (29 mol%), 86 CHOL (cholesterol, 17 mol%) and 73 CAL (14 mol%) at 310.15 K. Simulated with CHARMM36 with incorrect multiplicity in dihedrals and ECC ions in GROMACS 5.0 for 800 ns (60383 atoms). Deposited as NMRlipids Databank simulation 252 and available from https://doi.org/10.5281/zenodo.259376. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 40 mol%), 146 CLA (29 mol%), 86 CHOL (cholesterol, 17 mol%) and 73 CAL (14 mol%) + at 310.15 K. Simulated with CHARMM36 with incorrect multiplicity in dihedrals + and ECC ions in GROMACS 5.0 for 800 ns (60383 atoms). Deposited as NMRlipids Databank + simulation 252 and available from https://doi.org/10.5281/zenodo.259376. sameAs: https://doi.org/10.5281/zenodo.259376 datePublished: '2017-01-24' license: @@ -150,7 +156,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.259376 identifier: 10.5281/zenodo.259376 url: https://doi.org/10.5281/zenodo.259376 - name: Popc With Varying Amounts Of Cholesterol, 450 Mm Of Cacl_2. Charmm36 With Ecc-Scaled Ions + name: Popc With Varying Amounts Of Cholesterol, 450 Mm Of Cacl_2. Charmm36 With + Ecc-Scaled Ions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/3f8/237/3f82371d941cd4b7ef1f55268be8b31049048659/4c3d0df86a66ff5aeeca33bab80039851a5ad1bf/README.yaml b/Simulations/3f8/237/3f82371d941cd4b7ef1f55268be8b31049048659/4c3d0df86a66ff5aeeca33bab80039851a5ad1bf/README.yaml index bdc5137875..c63202591f 100644 --- a/Simulations/3f8/237/3f82371d941cd4b7ef1f55268be8b31049048659/4c3d0df86a66ff5aeeca33bab80039851a5ad1bf/README.yaml +++ b/Simulations/3f8/237/3f82371d941cd4b7ef1f55268be8b31049048659/4c3d0df86a66ff5aeeca33bab80039851a5ad1bf/README.yaml @@ -41,9 +41,12 @@ EXPERIMENT: FORMFACTOR: - 10.1021/acs.jctc.3c00648/1 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 300 K (Sage2.2.0 Espaloma Charges, GROMACS, 200 ns) [NMRlipids simulation 834] + name: Molecular dynamics trajectory of a POPC bilayer at 300 K (Sage2.2.0 Espaloma + Charges, GROMACS, 200 ns) [NMRlipids simulation 834] alternateName: POPCandTIP3P - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 300 K. Simulated with Sage2.2.0 Espaloma Charges in GROMACS for 200 ns (32512 atoms). Deposited as NMRlipids Databank simulation 834 and available from https://doi.org/10.5281/zenodo.15065566. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 300 K. Simulated with Sage2.2.0 Espaloma Charges in GROMACS for 200 ns (32512 + atoms). Deposited as NMRlipids Databank simulation 834 and available from https://doi.org/10.5281/zenodo.15065566. sameAs: https://doi.org/10.5281/zenodo.15065566 datePublished: '2025-03-21' license: diff --git a/Simulations/3f8/a6e/3f8a6eeb44aaeaff5c00d157ed0938d2e0d94048/48f5c2a60215696e2234f1a33488b1215e32e2cc/README.yaml b/Simulations/3f8/a6e/3f8a6eeb44aaeaff5c00d157ed0938d2e0d94048/48f5c2a60215696e2234f1a33488b1215e32e2cc/README.yaml index 10290fad63..4948e416a0 100644 --- a/Simulations/3f8/a6e/3f8a6eeb44aaeaff5c00d157ed0938d2e0d94048/48f5c2a60215696e2234f1a33488b1215e32e2cc/README.yaml +++ b/Simulations/3f8/a6e/3f8a6eeb44aaeaff5c00d157ed0938d2e0d94048/48f5c2a60215696e2234f1a33488b1215e32e2cc/README.yaml @@ -53,9 +53,13 @@ EXPERIMENT: - 10.1039/C4SM00066H/3 ID: 263 bioschema_properties: - name: Molecular dynamics trajectory of a POPS/SOD (50:50) bilayer at 298 K (CHARMM36-UA, GROMACS, 100 ns) [NMRlipids simulation 263] + name: Molecular dynamics trajectory of a POPS/SOD (50:50) bilayer at 298 K (CHARMM36-UA, + GROMACS, 100 ns) [NMRlipids simulation 263] alternateName: 128POPS_4480SOL_128SOD_298K_v2 - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 50 mol%) and 128 SOD (50 mol%) at 298 K. Simulated with CHARMM36-UA in GROMACS for 100 ns (22144 atoms). Deposited as NMRlipids Databank simulation 263 and available from https://doi.org/10.5281/zenodo.1129458. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, + 50 mol%) and 128 SOD (50 mol%) at 298 K. Simulated with CHARMM36-UA in GROMACS + for 100 ns (22144 atoms). Deposited as NMRlipids Databank simulation 263 and available + from https://doi.org/10.5281/zenodo.1129458. sameAs: https://doi.org/10.5281/zenodo.1129458 datePublished: '2017-12-24' license: diff --git a/Simulations/409/4d2/4094d27c1064905fc3fde0beadd3a78abb0de67d/ec0402b3b49905e63df6217b84ab8f7bedf23583/README.yaml b/Simulations/409/4d2/4094d27c1064905fc3fde0beadd3a78abb0de67d/ec0402b3b49905e63df6217b84ab8f7bedf23583/README.yaml index cfbf6e8ef6..2acbf22ebb 100644 --- a/Simulations/409/4d2/4094d27c1064905fc3fde0beadd3a78abb0de67d/ec0402b3b49905e63df6217b84ab8f7bedf23583/README.yaml +++ b/Simulations/409/4d2/4094d27c1064905fc3fde0beadd3a78abb0de67d/ec0402b3b49905e63df6217b84ab8f7bedf23583/README.yaml @@ -51,9 +51,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 56 bioschema_properties: - name: Molecular dynamics trajectory of a DOPC/CLA/SOD (81:9:9) bilayer at 310 K (CHARMM36, GROMACS 2019, 500 ns) [NMRlipids simulation 56] + name: Molecular dynamics trajectory of a DOPC/CLA/SOD (81:9:9) bilayer at 310 K + (CHARMM36, GROMACS 2019, 500 ns) [NMRlipids simulation 56] alternateName: 200DOPC_10000SOL_23SOD_23CLA - description: Molecular dynamics trajectory of a lipid bilayer of 200 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, 81 mol%), 23 CLA (9 mol%) and 23 SOD (9 mol%) at 310 K. Simulated with CHARMM36 in GROMACS 2019 for 500 ns (57646 atoms). Deposited as NMRlipids Databank simulation 56 and available from https://doi.org/10.5281/zenodo.3592499. + description: Molecular dynamics trajectory of a lipid bilayer of 200 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, + 81 mol%), 23 CLA (9 mol%) and 23 SOD (9 mol%) at 310 K. Simulated with CHARMM36 + in GROMACS 2019 for 500 ns (57646 atoms). Deposited as NMRlipids Databank simulation + 56 and available from https://doi.org/10.5281/zenodo.3592499. sameAs: https://doi.org/10.5281/zenodo.3592499 datePublished: '2019-12-24' license: diff --git a/Simulations/40e/b28/40eb28cd6e468287a13f7ef3ce18a63d334210dd/c46c0e78ea3a649685d1ceca84b31b3ed6d67fd2/README.yaml b/Simulations/40e/b28/40eb28cd6e468287a13f7ef3ce18a63d334210dd/c46c0e78ea3a649685d1ceca84b31b3ed6d67fd2/README.yaml index c5bad79649..b99498135d 100644 --- a/Simulations/40e/b28/40eb28cd6e468287a13f7ef3ce18a63d334210dd/c46c0e78ea3a649685d1ceca84b31b3ed6d67fd2/README.yaml +++ b/Simulations/40e/b28/40eb28cd6e468287a13f7ef3ce18a63d334210dd/c46c0e78ea3a649685d1ceca84b31b3ed6d67fd2/README.yaml @@ -42,9 +42,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 711 bioschema_properties: - name: Molecular dynamics trajectory of a DOPC bilayer at 298.15 K (CHARMM36, GROMACS 2021, 1001 ns) [NMRlipids simulation 711] + name: Molecular dynamics trajectory of a DOPC bilayer at 298.15 K (CHARMM36, GROMACS + 2021, 1001 ns) [NMRlipids simulation 711] alternateName: DOPC_M - description: Molecular dynamics trajectory of a lipid bilayer of 256 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) at 298.15 K. Simulated with CHARMM36 in GROMACS 2021 for 1001 ns (73728 atoms). Deposited as NMRlipids Databank simulation 711 and available from https://doi.org/10.5281/zenodo.7103807. + description: Molecular dynamics trajectory of a lipid bilayer of 256 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) + at 298.15 K. Simulated with CHARMM36 in GROMACS 2021 for 1001 ns (73728 atoms). + Deposited as NMRlipids Databank simulation 711 and available from https://doi.org/10.5281/zenodo.7103807. sameAs: https://doi.org/10.5281/zenodo.7103807 datePublished: '2022-09-22' license: diff --git a/Simulations/412/bcb/412bcbbdcff3702a98568d7f474a475802eda741/5d2e72df58fa8ac6c3a88a261b25813d9ba814bf/README.yaml b/Simulations/412/bcb/412bcbbdcff3702a98568d7f474a475802eda741/5d2e72df58fa8ac6c3a88a261b25813d9ba814bf/README.yaml index 1878bb8689..67548ae566 100644 --- a/Simulations/412/bcb/412bcbbdcff3702a98568d7f474a475802eda741/5d2e72df58fa8ac6c3a88a261b25813d9ba814bf/README.yaml +++ b/Simulations/412/bcb/412bcbbdcff3702a98568d7f474a475802eda741/5d2e72df58fa8ac6c3a88a261b25813d9ba814bf/README.yaml @@ -56,9 +56,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 407 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL/CLA/SOD (68:17:7:7) bilayer at 310.15 K (CHARMM36, GROMACS 5.0, 200 ns) [NMRlipids simulation 407] + name: Molecular dynamics trajectory of a POPC/CHOL/CLA/SOD (68:17:7:7) bilayer at + 310.15 K (CHARMM36, GROMACS 5.0, 200 ns) [NMRlipids simulation 407] alternateName: 50CHOL_200POPC_9000SOL_21SOD_21CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 68 mol%), 50 CHOL (cholesterol, 17 mol%), 21 CLA (7 mol%) and 21 SOD (7 mol%) at 310.15 K. Simulated with CHARMM36 in GROMACS 5.0 for 200 ns (57542 atoms). Deposited as NMRlipids Databank simulation 407 and available from https://doi.org/10.5281/zenodo.259392. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 68 mol%), 50 CHOL (cholesterol, 17 mol%), 21 CLA (7 mol%) and 21 SOD (7 mol%) + at 310.15 K. Simulated with CHARMM36 in GROMACS 5.0 for 200 ns (57542 atoms). + Deposited as NMRlipids Databank simulation 407 and available from https://doi.org/10.5281/zenodo.259392. sameAs: https://doi.org/10.5281/zenodo.259392 datePublished: '2017-01-24' license: @@ -148,7 +152,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.259392 identifier: 10.5281/zenodo.259392 url: https://doi.org/10.5281/zenodo.259392 - name: Popc With Varying Amounts Of Cholesterol, 130 Mm Of Nacl. Charmm36 With Default Charmm Ions + name: Popc With Varying Amounts Of Cholesterol, 130 Mm Of Nacl. Charmm36 With + Default Charmm Ions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/415/930/41593025f50adfceb2c888fed44afe0b1b7fe8da/34bafde4722aae82cc5972f9e30a54065d67159a/README.yaml b/Simulations/415/930/41593025f50adfceb2c888fed44afe0b1b7fe8da/34bafde4722aae82cc5972f9e30a54065d67159a/README.yaml index ceba98caae..6bebe6dac0 100644 --- a/Simulations/415/930/41593025f50adfceb2c888fed44afe0b1b7fe8da/34bafde4722aae82cc5972f9e30a54065d67159a/README.yaml +++ b/Simulations/415/930/41593025f50adfceb2c888fed44afe0b1b7fe8da/34bafde4722aae82cc5972f9e30a54065d67159a/README.yaml @@ -46,9 +46,12 @@ EXPERIMENT: - 10.1021/jp511159q/1 ID: 414 bioschema_properties: - name: Molecular dynamics trajectory of a POPE bilayer at 310 K (Slipids, GROMACS 2018.3, 100 ns) [NMRlipids simulation 414] + name: Molecular dynamics trajectory of a POPE bilayer at 310 K (Slipids, GROMACS + 2018.3, 100 ns) [NMRlipids simulation 414] alternateName: 500POPE_25000SOL_310K - description: Molecular dynamics trajectory of a lipid bilayer of 500 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) at 310 K. Simulated with Slipids in GROMACS 2018.3 for 100 ns (137500 atoms). Deposited as NMRlipids Databank simulation 414 and available from https://doi.org/10.5281/zenodo.3231342. + description: Molecular dynamics trajectory of a lipid bilayer of 500 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) + at 310 K. Simulated with Slipids in GROMACS 2018.3 for 100 ns (137500 atoms). + Deposited as NMRlipids Databank simulation 414 and available from https://doi.org/10.5281/zenodo.3231342. sameAs: https://doi.org/10.5281/zenodo.3231342 datePublished: '2019-05-27' license: diff --git a/Simulations/415/c8f/415c8f2ddad11397599f25a263dd04dc753fa634/8bbabd9e99e5444eeafff849c4c621caae5f92a3/README.yaml b/Simulations/415/c8f/415c8f2ddad11397599f25a263dd04dc753fa634/8bbabd9e99e5444eeafff849c4c621caae5f92a3/README.yaml index 224156972e..8533b74f3c 100644 --- a/Simulations/415/c8f/415c8f2ddad11397599f25a263dd04dc753fa634/8bbabd9e99e5444eeafff849c4c621caae5f92a3/README.yaml +++ b/Simulations/415/c8f/415c8f2ddad11397599f25a263dd04dc753fa634/8bbabd9e99e5444eeafff849c4c621caae5f92a3/README.yaml @@ -58,9 +58,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 413 bioschema_properties: - name: Molecular dynamics trajectory of a POPG/SOD/POPE (43:43:14) bilayer at 310 K (GROMOS-CKP, GROMACS 2018.3, 100 ns) [NMRlipids simulation 413] + name: Molecular dynamics trajectory of a POPG/SOD/POPE (43:43:14) bilayer at 310 + K (GROMOS-CKP, GROMACS 2018.3, 100 ns) [NMRlipids simulation 413] alternateName: 374POPG_126POPE_25000SOL_374SOD_310K - description: Molecular dynamics trajectory of a lipid bilayer of 374 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 43 mol%), 374 SOD (43 mol%) and 126 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 14 mol%) at 310 K. Simulated with GROMOS-CKP in GROMACS 2018.3 for 100 ns (101748 atoms). Deposited as NMRlipids Databank simulation 413 and available from https://doi.org/10.5281/zenodo.3267234. + description: Molecular dynamics trajectory of a lipid bilayer of 374 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, + 43 mol%), 374 SOD (43 mol%) and 126 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, + 14 mol%) at 310 K. Simulated with GROMOS-CKP in GROMACS 2018.3 for 100 ns (101748 + atoms). Deposited as NMRlipids Databank simulation 413 and available from https://doi.org/10.5281/zenodo.3267234. sameAs: https://doi.org/10.5281/zenodo.3267234 datePublished: '2019-07-03' license: diff --git a/Simulations/417/57f/41757fcae2788b4acce2e9b601bfa7c768e8e7b0/fbeaaf46fef02433daa4c430bec6db90de985429/README.yaml b/Simulations/417/57f/41757fcae2788b4acce2e9b601bfa7c768e8e7b0/fbeaaf46fef02433daa4c430bec6db90de985429/README.yaml index c3654ad434..5fbe7caf89 100644 --- a/Simulations/417/57f/41757fcae2788b4acce2e9b601bfa7c768e8e7b0/fbeaaf46fef02433daa4c430bec6db90de985429/README.yaml +++ b/Simulations/417/57f/41757fcae2788b4acce2e9b601bfa7c768e8e7b0/fbeaaf46fef02433daa4c430bec6db90de985429/README.yaml @@ -41,9 +41,12 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 462 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 303 K (CHARMM36, GROMACS 5.0.6, 500 ns) [NMRlipids simulation 462] + name: Molecular dynamics trajectory of a POPC bilayer at 303 K (CHARMM36, GROMACS + 5.0.6, 500 ns) [NMRlipids simulation 462] alternateName: 128POPC_5120SOL_8A-switch_v3 - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 303 K. Simulated with CHARMM36 in GROMACS 5.0.6 for 500 ns (32512 atoms). Deposited as NMRlipids Databank simulation 462 and available from https://doi.org/10.5281/zenodo.164206. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 303 K. Simulated with CHARMM36 in GROMACS 5.0.6 for 500 ns (32512 atoms). Deposited + as NMRlipids Databank simulation 462 and available from https://doi.org/10.5281/zenodo.164206. sameAs: https://doi.org/10.5281/zenodo.164206 datePublished: '2016-11-01' license: diff --git a/Simulations/41a/fb0/41afb0b8c74214ba9397c556a8b42fb02431ff34/eac51afd286254d306ef2f48f7c232593b888e70/README.yaml b/Simulations/41a/fb0/41afb0b8c74214ba9397c556a8b42fb02431ff34/eac51afd286254d306ef2f48f7c232593b888e70/README.yaml index afbeedae4f..ff4d87ecf1 100644 --- a/Simulations/41a/fb0/41afb0b8c74214ba9397c556a8b42fb02431ff34/eac51afd286254d306ef2f48f7c232593b888e70/README.yaml +++ b/Simulations/41a/fb0/41afb0b8c74214ba9397c556a8b42fb02431ff34/eac51afd286254d306ef2f48f7c232593b888e70/README.yaml @@ -57,9 +57,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 283 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL/CLA/SOD (68:17:7:7) bilayer at 310 K (Slipids for lipids and Smith & Dang for ions, GROMACS 4.6, 200 ns) [NMRlipids simulation 283] + name: Molecular dynamics trajectory of a POPC/CHOL/CLA/SOD (68:17:7:7) bilayer at + 310 K (Slipids for lipids and Smith & Dang for ions, GROMACS 4.6, 200 ns) [NMRlipids + simulation 283] alternateName: 50CHOL_200POPC_9000SOL_21SOD_21CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 68 mol%), 50 CHOL (cholesterol, 17 mol%), 21 CLA (7 mol%) and 21 SOD (7 mol%) at 310 K. Simulated with Slipids for lipids and Smith & Dang for ions in GROMACS 4.6 for 200 ns (57542 atoms). Deposited as NMRlipids Databank simulation 283 and available from https://doi.org/10.5281/zenodo.259335. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 68 mol%), 50 CHOL (cholesterol, 17 mol%), 21 CLA (7 mol%) and 21 SOD (7 mol%) + at 310 K. Simulated with Slipids for lipids and Smith & Dang for ions in GROMACS + 4.6 for 200 ns (57542 atoms). Deposited as NMRlipids Databank simulation 283 and + available from https://doi.org/10.5281/zenodo.259335. sameAs: https://doi.org/10.5281/zenodo.259335 datePublished: '2017-01-24' license: @@ -149,7 +155,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.259335 identifier: 10.5281/zenodo.259335 url: https://doi.org/10.5281/zenodo.259335 - name: Popc With Varying Amounts Of Cholesterol, 130 Mm Of Nacl. Slipids With Ions By Smith & Dang + name: Popc With Varying Amounts Of Cholesterol, 130 Mm Of Nacl. Slipids With Ions + By Smith & Dang publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/41f/767/41f76702bdd70e5f78dc1d784ebad5c25f2f9285/fa9d450aa3b7767a7279675d18f70cfd6762117f/README.yaml b/Simulations/41f/767/41f76702bdd70e5f78dc1d784ebad5c25f2f9285/fa9d450aa3b7767a7279675d18f70cfd6762117f/README.yaml index de2b475667..a5ffe4a38e 100644 --- a/Simulations/41f/767/41f76702bdd70e5f78dc1d784ebad5c25f2f9285/fa9d450aa3b7767a7279675d18f70cfd6762117f/README.yaml +++ b/Simulations/41f/767/41f76702bdd70e5f78dc1d784ebad5c25f2f9285/fa9d450aa3b7767a7279675d18f70cfd6762117f/README.yaml @@ -61,9 +61,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 447 bioschema_properties: - name: Molecular dynamics trajectory of a SOD/POPG/POPE/CLA (44:38:13:5) bilayer at 310 K (GROMOS-CKP, GROMACS 5.1.2, 100 ns) [NMRlipids simulation 447] + name: Molecular dynamics trajectory of a SOD/POPG/POPE/CLA (44:38:13:5) bilayer + at 310 K (GROMOS-CKP, GROMACS 5.1.2, 100 ns) [NMRlipids simulation 447] alternateName: 374POPG_126POPE_25000SOL_423SOD_49CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 423 SOD (44 mol%), 374 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 38 mol%), 126 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 13 mol%) and 49 CLA (5 mol%) at 310 K. Simulated with GROMOS-CKP in GROMACS 5.1.2 for 100 ns (101846 atoms). Deposited as NMRlipids Databank simulation 447 and available from https://doi.org/10.5281/zenodo.2580158. + description: Molecular dynamics trajectory of a lipid bilayer of 423 SOD (44 mol%), + 374 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 38 mol%), 126 POPE + (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 13 mol%) and 49 CLA (5 + mol%) at 310 K. Simulated with GROMOS-CKP in GROMACS 5.1.2 for 100 ns (101846 + atoms). Deposited as NMRlipids Databank simulation 447 and available from https://doi.org/10.5281/zenodo.2580158. sameAs: https://doi.org/10.5281/zenodo.2580158 datePublished: '2019-02-28' license: @@ -156,7 +161,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.2580158 identifier: 10.5281/zenodo.2580158 url: https://doi.org/10.5281/zenodo.2580158 - name: GROMOS-CKP POPG-POPE 3:1 Bilayer Simulation (Last 100 ns, 150 mM NaCl, 310 K ) + name: GROMOS-CKP POPG-POPE 3:1 Bilayer Simulation (Last 100 ns, 150 mM NaCl, 310 + K ) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/430/089/430089b8f67afdbce1c26510edb3772a4f3c43bf/a98ab4e14794c70e9a03e1f8d56b7e95106cf209/README.yaml b/Simulations/430/089/430089b8f67afdbce1c26510edb3772a4f3c43bf/a98ab4e14794c70e9a03e1f8d56b7e95106cf209/README.yaml index 1099873a6d..9ebc1fb7f8 100644 --- a/Simulations/430/089/430089b8f67afdbce1c26510edb3772a4f3c43bf/a98ab4e14794c70e9a03e1f8d56b7e95106cf209/README.yaml +++ b/Simulations/430/089/430089b8f67afdbce1c26510edb3772a4f3c43bf/a98ab4e14794c70e9a03e1f8d56b7e95106cf209/README.yaml @@ -38,9 +38,12 @@ EXPERIMENT: FORMFACTOR: - 10.1016/j.bbamem.2011.07.022/8 bioschema_properties: - name: Molecular dynamics trajectory of a DLPC bilayer at 323 K (CHARMM36/LJ-PME, GROMACS Gromacs 2022, 100 ns) [NMRlipids simulation 917] + name: Molecular dynamics trajectory of a DLPC bilayer at 323 K (CHARMM36/LJ-PME, + GROMACS Gromacs 2022, 100 ns) [NMRlipids simulation 917] alternateName: Fully hydrated DLPC bilayer in SPC/E water (LJ-PME) - description: Molecular dynamics trajectory of a lipid bilayer of 100 DLPC (1,2-dilauroyl-sn-glycero-3-phosphocholine) at 323 K. Simulated with CHARMM36/LJ-PME in GROMACS Gromacs 2022 for 100 ns (23542 atoms). Deposited as NMRlipids Databank simulation 917 and available from https://doi.org/10.5281/zenodo.20579050. + description: Molecular dynamics trajectory of a lipid bilayer of 100 DLPC (1,2-dilauroyl-sn-glycero-3-phosphocholine) + at 323 K. Simulated with CHARMM36/LJ-PME in GROMACS Gromacs 2022 for 100 ns (23542 + atoms). Deposited as NMRlipids Databank simulation 917 and available from https://doi.org/10.5281/zenodo.20579050. sameAs: https://doi.org/10.5281/zenodo.20579050 datePublished: '2026-06-07' license: @@ -131,7 +134,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.20579050 identifier: 10.5281/zenodo.20579050 url: https://doi.org/10.5281/zenodo.20579050 - name: Fully hydrated DLPC bilayer at different temperatures simulated using CHARMM36 with LJ-PME and LJ-cutoff + name: Fully hydrated DLPC bilayer at different temperatures simulated using CHARMM36 + with LJ-PME and LJ-cutoff publisher: Zenodo _source: api: datacite diff --git a/Simulations/431/280/4312804073e3bd4cf052fac381c0df939edce466/33b1dae354013a5cecff1d9c6a1343c880ccc595/README.yaml b/Simulations/431/280/4312804073e3bd4cf052fac381c0df939edce466/33b1dae354013a5cecff1d9c6a1343c880ccc595/README.yaml index be4b1e9e4b..fe236ea491 100644 --- a/Simulations/431/280/4312804073e3bd4cf052fac381c0df939edce466/33b1dae354013a5cecff1d9c6a1343c880ccc595/README.yaml +++ b/Simulations/431/280/4312804073e3bd4cf052fac381c0df939edce466/33b1dae354013a5cecff1d9c6a1343c880ccc595/README.yaml @@ -56,9 +56,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 460 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPS/SOD (71:14:14) bilayer at 298 K (GROMOS-CKP, GROMOS NH3 charges and PME, GROMACS, 100 ns) [NMRlipids simulation 460] + name: Molecular dynamics trajectory of a POPC/POPS/SOD (71:14:14) bilayer at 298 + K (GROMOS-CKP, GROMOS NH3 charges and PME, GROMACS, 100 ns) [NMRlipids simulation + 460] alternateName: 110POPC_22POPS_4620SOL_22SOD_298K_GROMOS-CKP_v2 - description: Molecular dynamics trajectory of a lipid bilayer of 110 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 71 mol%), 22 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 14 mol%) and 22 SOD (14 mol%) at 298 K. Simulated with GROMOS-CKP, GROMOS NH3 charges and PME in GROMACS for 100 ns (20812 atoms). Deposited as NMRlipids Databank simulation 460 and available from https://doi.org/10.5281/zenodo.1283333. + description: Molecular dynamics trajectory of a lipid bilayer of 110 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 71 mol%), 22 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 14 mol%) + and 22 SOD (14 mol%) at 298 K. Simulated with GROMOS-CKP, GROMOS NH3 charges and + PME in GROMACS for 100 ns (20812 atoms). Deposited as NMRlipids Databank simulation + 460 and available from https://doi.org/10.5281/zenodo.1283333. sameAs: https://doi.org/10.5281/zenodo.1283333 datePublished: '2018-06-05' license: @@ -147,7 +153,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1283333 identifier: 10.5281/zenodo.1283333 url: https://doi.org/10.5281/zenodo.1283333 - name: Gromos-Ckp Pops/Popc Simulations (Versions 1 And 2) 298 K With Gromos Nh3 Charges And Pme + name: Gromos-Ckp Pops/Popc Simulations (Versions 1 And 2) 298 K With Gromos Nh3 + Charges And Pme publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/436/81a/43681aac9491f23ea55f7cdf39b5df580f8e0279/c89a204992c50aa5c464e5ef5b4981c3b24fbe13/README.yaml b/Simulations/436/81a/43681aac9491f23ea55f7cdf39b5df580f8e0279/c89a204992c50aa5c464e5ef5b4981c3b24fbe13/README.yaml index 5f595cf544..cd4c4ad06d 100644 --- a/Simulations/436/81a/43681aac9491f23ea55f7cdf39b5df580f8e0279/c89a204992c50aa5c464e5ef5b4981c3b24fbe13/README.yaml +++ b/Simulations/436/81a/43681aac9491f23ea55f7cdf39b5df580f8e0279/c89a204992c50aa5c464e5ef5b4981c3b24fbe13/README.yaml @@ -47,9 +47,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 13 bioschema_properties: - name: Molecular dynamics trajectory of a CHOL/POPC (50:50) bilayer at 303 K (CHARMM36, GROMACS 2020.1, 840 ns) [NMRlipids simulation 13] + name: Molecular dynamics trajectory of a CHOL/POPC (50:50) bilayer at 303 K (CHARMM36, + GROMACS 2020.1, 840 ns) [NMRlipids simulation 13] alternateName: 122CHOL_122POPC_9760SOL_303K - description: Molecular dynamics trajectory of a lipid bilayer of 122 CHOL (cholesterol, 50 mol%) and 122 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 50 mol%) at 303 K. Simulated with CHARMM36 in GROMACS 2020.1 for 840 ns (54656 atoms). Deposited as NMRlipids Databank simulation 13 and available from https://doi.org/10.5281/zenodo.4071264. + description: Molecular dynamics trajectory of a lipid bilayer of 122 CHOL (cholesterol, + 50 mol%) and 122 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 50 mol%) + at 303 K. Simulated with CHARMM36 in GROMACS 2020.1 for 840 ns (54656 atoms). + Deposited as NMRlipids Databank simulation 13 and available from https://doi.org/10.5281/zenodo.4071264. sameAs: https://doi.org/10.5281/zenodo.4071264 datePublished: '2020-10-07' license: @@ -139,7 +143,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.4071264 identifier: 10.5281/zenodo.4071264 url: https://doi.org/10.5281/zenodo.4071264 - name: CHARMM36 simulations of pure POPC bilayer and a bilayer containing 50% of cholesterol, T=303K + name: CHARMM36 simulations of pure POPC bilayer and a bilayer containing 50% of + cholesterol, T=303K publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/43e/a38/43ea38445266fcf9cca6cacb2331a09efcd123e0/0c14671bb338f2f09e32ccd0d375e0583d6db73f/README.yaml b/Simulations/43e/a38/43ea38445266fcf9cca6cacb2331a09efcd123e0/0c14671bb338f2f09e32ccd0d375e0583d6db73f/README.yaml index aa0243ce23..80a88ee579 100644 --- a/Simulations/43e/a38/43ea38445266fcf9cca6cacb2331a09efcd123e0/0c14671bb338f2f09e32ccd0d375e0583d6db73f/README.yaml +++ b/Simulations/43e/a38/43ea38445266fcf9cca6cacb2331a09efcd123e0/0c14671bb338f2f09e32ccd0d375e0583d6db73f/README.yaml @@ -53,9 +53,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/9 ID: 712 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (53:47) bilayer at 298.15 K (Slipids, GROMACS 2021, 1001 ns) [NMRlipids simulation 712] + name: Molecular dynamics trajectory of a POPC/CHOL (53:47) bilayer at 298.15 K (Slipids, + GROMACS 2021, 1001 ns) [NMRlipids simulation 712] alternateName: Slipids_POPC_CHOL47_M - description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 53 mol%) and 224 CHOL (cholesterol, 47 mol%) at 298.15 K. Simulated with Slipids in GROMACS 2021 for 1001 ns (122880 atoms). Deposited as NMRlipids Databank simulation 712 and available from https://doi.org/10.5281/zenodo.7022749. + description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 53 mol%) and 224 CHOL (cholesterol, 47 mol%) at 298.15 K. Simulated with Slipids + in GROMACS 2021 for 1001 ns (122880 atoms). Deposited as NMRlipids Databank simulation + 712 and available from https://doi.org/10.5281/zenodo.7022749. sameAs: https://doi.org/10.5281/zenodo.7022749 datePublished: '2022-08-23' license: diff --git a/Simulations/445/4c3/4454c358ea09af737d35da519a83406894e4d560/328e389a48d421079fb259a6ea2d71a0b51e0906/README.yaml b/Simulations/445/4c3/4454c358ea09af737d35da519a83406894e4d560/328e389a48d421079fb259a6ea2d71a0b51e0906/README.yaml index 7ecd682f02..70f873f022 100644 --- a/Simulations/445/4c3/4454c358ea09af737d35da519a83406894e4d560/328e389a48d421079fb259a6ea2d71a0b51e0906/README.yaml +++ b/Simulations/445/4c3/4454c358ea09af737d35da519a83406894e4d560/328e389a48d421079fb259a6ea2d71a0b51e0906/README.yaml @@ -58,9 +58,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 266 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CER/CLA/SOD (63:16:11:11) bilayer at 310 K (CHARMM36, GROMACS 2016.1, 3012 ns) [NMRlipids simulation 266] + name: Molecular dynamics trajectory of a POPC/CER/CLA/SOD (63:16:11:11) bilayer + at 310 K (CHARMM36, GROMACS 2016.1, 3012 ns) [NMRlipids simulation 266] alternateName: 512POPC_128CER_32000SOL_86SOD_86CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 512 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 63 mol%), 128 CER (N-palmitoyl-D-erythro-sphingosine, 16 mol%), 86 CLA (11 mol%) and 86 SOD (11 mol%) at 310 K. Simulated with CHARMM36 in GROMACS 2016.1 for 3012 ns (178220 atoms). Deposited as NMRlipids Databank simulation 266 and available from https://doi.org/10.5281/zenodo.3248612. + description: Molecular dynamics trajectory of a lipid bilayer of 512 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 63 mol%), 128 CER (N-palmitoyl-D-erythro-sphingosine, 16 mol%), 86 CLA (11 mol%) + and 86 SOD (11 mol%) at 310 K. Simulated with CHARMM36 in GROMACS 2016.1 for 3012 + ns (178220 atoms). Deposited as NMRlipids Databank simulation 266 and available + from https://doi.org/10.5281/zenodo.3248612. sameAs: https://doi.org/10.5281/zenodo.3248612 datePublished: '2019-06-18' license: diff --git a/Simulations/448/ee0/448ee0f82614e380ddcc95972779e6193e2a6d4b/e5f35501e12d748ed84c346a48680e77d5ff26c3/README.yaml b/Simulations/448/ee0/448ee0f82614e380ddcc95972779e6193e2a6d4b/e5f35501e12d748ed84c346a48680e77d5ff26c3/README.yaml index 08a007d0ad..a2e1b19a20 100644 --- a/Simulations/448/ee0/448ee0f82614e380ddcc95972779e6193e2a6d4b/e5f35501e12d748ed84c346a48680e77d5ff26c3/README.yaml +++ b/Simulations/448/ee0/448ee0f82614e380ddcc95972779e6193e2a6d4b/e5f35501e12d748ed84c346a48680e77d5ff26c3/README.yaml @@ -55,9 +55,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 223 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPS/POT (33:33:33) bilayer at 298 K (ECC-lipids, SPC/E water model, ECC-ions, GROMACS 2018.0, 987 ns) [NMRlipids simulation 223] + name: Molecular dynamics trajectory of a POPC/POPS/POT (33:33:33) bilayer at 298 + K (ECC-lipids, SPC/E water model, ECC-ions, GROMACS 2018.0, 987 ns) [NMRlipids + simulation 223] alternateName: 64POPS_64POPC_5253SOL_64POT_298K_ECC-lipid - description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 33 mol%), 64 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 33 mol%) and 64 POT (33 mol%) at 298 K. Simulated with ECC-lipids, SPC/E water model, ECC-ions in GROMACS 2018.0 for 987 ns (32527 atoms). Deposited as NMRlipids Databank simulation 223 and available from https://doi.org/10.5281/zenodo.1488094. + description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 33 mol%), 64 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 33 mol%) + and 64 POT (33 mol%) at 298 K. Simulated with ECC-lipids, SPC/E water model, ECC-ions + in GROMACS 2018.0 for 987 ns (32527 atoms). Deposited as NMRlipids Databank simulation + 223 and available from https://doi.org/10.5281/zenodo.1488094. sameAs: https://doi.org/10.5281/zenodo.1488094 datePublished: '2018-11-14' license: @@ -148,7 +154,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1488094 identifier: 10.5281/zenodo.1488094 url: https://doi.org/10.5281/zenodo.1488094 - name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS (various mixtures) with ECC-lipids force field, and Na+ (K+) counterions + name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS + (various mixtures) with ECC-lipids force field, and Na+ (K+) counterions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/450/dbe/450dbebb97c739940eead3ccf37287aacdf14d93/0a833ef3e11ab9df384abd7e4cbcfcf3a5d16a72/README.yaml b/Simulations/450/dbe/450dbebb97c739940eead3ccf37287aacdf14d93/0a833ef3e11ab9df384abd7e4cbcfcf3a5d16a72/README.yaml index 60e9221c4f..1ac0b46018 100644 --- a/Simulations/450/dbe/450dbebb97c739940eead3ccf37287aacdf14d93/0a833ef3e11ab9df384abd7e4cbcfcf3a5d16a72/README.yaml +++ b/Simulations/450/dbe/450dbebb97c739940eead3ccf37287aacdf14d93/0a833ef3e11ab9df384abd7e4cbcfcf3a5d16a72/README.yaml @@ -50,9 +50,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 489 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/CLA/SOD (82:9:9) bilayer at 322 K (CHARMM36, GROMACS 5.0.4, 700 ns) [NMRlipids simulation 489] + name: Molecular dynamics trajectory of a DPPC/CLA/SOD (82:9:9) bilayer at 322 K + (CHARMM36, GROMACS 5.0.4, 700 ns) [NMRlipids simulation 489] alternateName: DPPC_512_NaCl_150mM_322K_v-rescale - description: Molecular dynamics trajectory of a lipid bilayer of 512 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 82 mol%), 55 CLA (9 mol%) and 55 SOD (9 mol%) at 322 K. Simulated with CHARMM36 in GROMACS 5.0.4 for 700 ns (128110 atoms). Deposited as NMRlipids Databank simulation 489 and available from https://doi.org/10.5281/zenodo.1009027. + description: Molecular dynamics trajectory of a lipid bilayer of 512 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 82 mol%), 55 CLA (9 mol%) and 55 SOD (9 mol%) at 322 K. Simulated with CHARMM36 + in GROMACS 5.0.4 for 700 ns (128110 atoms). Deposited as NMRlipids Databank simulation + 489 and available from https://doi.org/10.5281/zenodo.1009027. sameAs: https://doi.org/10.5281/zenodo.1009027 datePublished: '2017-10-11' license: diff --git a/Simulations/451/273/451273d9c4af697bf8200f684ed2107db31e2035/7df2979b9ebfbcf788868c2a567169f0c5ee3548/README.yaml b/Simulations/451/273/451273d9c4af697bf8200f684ed2107db31e2035/7df2979b9ebfbcf788868c2a567169f0c5ee3548/README.yaml index 2a19d10e05..71a4f18980 100644 --- a/Simulations/451/273/451273d9c4af697bf8200f684ed2107db31e2035/7df2979b9ebfbcf788868c2a567169f0c5ee3548/README.yaml +++ b/Simulations/451/273/451273d9c4af697bf8200f684ed2107db31e2035/7df2979b9ebfbcf788868c2a567169f0c5ee3548/README.yaml @@ -48,9 +48,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 96 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (89:11) bilayer at 310 K (MacRog, GROMACS 4.6, 500 ns) [NMRlipids simulation 96] + name: Molecular dynamics trajectory of a POPC/CHOL (89:11) bilayer at 310 K (MacRog, + GROMACS 4.6, 500 ns) [NMRlipids simulation 96] alternateName: 114POPC_14CHOL_6400SOL_310K - description: Molecular dynamics trajectory of a lipid bilayer of 114 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 89 mol%) and 14 CHOL (cholesterol, 11 mol%) at 310 K. Simulated with MacRog in GROMACS 4.6 for 500 ns (35512 atoms). Deposited as NMRlipids Databank simulation 96 and available from https://doi.org/10.5281/zenodo.3252052. + description: Molecular dynamics trajectory of a lipid bilayer of 114 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 89 mol%) and 14 CHOL (cholesterol, 11 mol%) at 310 K. Simulated with MacRog in + GROMACS 4.6 for 500 ns (35512 atoms). Deposited as NMRlipids Databank simulation + 96 and available from https://doi.org/10.5281/zenodo.3252052. sameAs: https://doi.org/10.5281/zenodo.3252052 datePublished: '2015-01-11' license: @@ -143,7 +147,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3252052 identifier: 10.5281/zenodo.3252052 url: https://doi.org/10.5281/zenodo.3252052 - name: POPC/Cholesterol @ 310K. 0, 10, 40, 50 and 60 mol-% cholesterol. Model by Maciejewski and Rog + name: POPC/Cholesterol @ 310K. 0, 10, 40, 50 and 60 mol-% cholesterol. Model by + Maciejewski and Rog publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/456/b6f/456b6f38c019229459ed3f4de1272ce51e9beaf6/fa29798b5c1cbeac034e89bfd1b5e61adb840567/README.yaml b/Simulations/456/b6f/456b6f38c019229459ed3f4de1272ce51e9beaf6/fa29798b5c1cbeac034e89bfd1b5e61adb840567/README.yaml index 1bd9e87e89..b9668dd946 100644 --- a/Simulations/456/b6f/456b6f38c019229459ed3f4de1272ce51e9beaf6/fa29798b5c1cbeac034e89bfd1b5e61adb840567/README.yaml +++ b/Simulations/456/b6f/456b6f38c019229459ed3f4de1272ce51e9beaf6/fa29798b5c1cbeac034e89bfd1b5e61adb840567/README.yaml @@ -63,9 +63,16 @@ EXPERIMENT: FORMFACTOR: [] ID: 434 bioschema_properties: - name: Molecular dynamics trajectory of a CLA/POT/POPC/POPS/SOD (40:40:14:3:3) bilayer at 298 K (Lipid17 and Dang ions, GROMACS 2018.0, 1000 ns) [NMRlipids simulation 434] + name: Molecular dynamics trajectory of a CLA/POT/POPC/POPS/SOD (40:40:14:3:3) bilayer + at 298 K (Lipid17 and Dang ions, GROMACS 2018.0, 1000 ns) [NMRlipids simulation + 434] alternateName: 12POPS_60POPC_3213SOL_12SOD_174POT_174CLA_298K - description: Molecular dynamics trajectory of a lipid bilayer of 174 CLA (40 mol%), 174 POT (40 mol%), 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 14 mol%), 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 3 mol%) and 12 SOD (3 mol%) at 298 K. Simulated with Lipid17 and Dang ions in GROMACS 2018.0 for 1000 ns (19563 atoms). Deposited as NMRlipids Databank simulation 434 and available from https://doi.org/10.5281/zenodo.1487895. + description: Molecular dynamics trajectory of a lipid bilayer of 174 CLA (40 mol%), + 174 POT (40 mol%), 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 14 mol%), 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 3 mol%) + and 12 SOD (3 mol%) at 298 K. Simulated with Lipid17 and Dang ions in GROMACS + 2018.0 for 1000 ns (19563 atoms). Deposited as NMRlipids Databank simulation 434 + and available from https://doi.org/10.5281/zenodo.1487895. sameAs: https://doi.org/10.5281/zenodo.1487895 datePublished: '2018-11-14' license: @@ -158,7 +165,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1487895 identifier: 10.5281/zenodo.1487895 url: https://doi.org/10.5281/zenodo.1487895 - name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS with the lipid17 force field, NaCl and KCl salt concentrations + name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS + with the lipid17 force field, NaCl and KCl salt concentrations publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/466/8e6/4668e6f280555fd75c047ba4f9fc223b3c74a8ab/f6c7d7550355e644ed9e1cb65d185527d6b0f35c/README.yaml b/Simulations/466/8e6/4668e6f280555fd75c047ba4f9fc223b3c74a8ab/f6c7d7550355e644ed9e1cb65d185527d6b0f35c/README.yaml index 09f6adb1c5..0dfe468f03 100644 --- a/Simulations/466/8e6/4668e6f280555fd75c047ba4f9fc223b3c74a8ab/f6c7d7550355e644ed9e1cb65d185527d6b0f35c/README.yaml +++ b/Simulations/466/8e6/4668e6f280555fd75c047ba4f9fc223b3c74a8ab/f6c7d7550355e644ed9e1cb65d185527d6b0f35c/README.yaml @@ -63,9 +63,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 531 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPS/SOD/CLA/CAL (61:12:12:10:5) bilayer at 298 K (ECC-lipids, SPC/E water model, ECC-ions, GROMACS 2018.0, 1000 ns) [NMRlipids simulation 531] + name: Molecular dynamics trajectory of a POPC/POPS/SOD/CLA/CAL (61:12:12:10:5) bilayer + at 298 K (ECC-lipids, SPC/E water model, ECC-ions, GROMACS 2018.0, 1000 ns) [NMRlipids + simulation 531] alternateName: 12POPS_60POPC_3561SOL_5CAL_10CLA_12SOD_298K - description: Molecular dynamics trajectory of a lipid bilayer of 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 61 mol%), 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 12 mol%), 12 SOD (12 mol%), 10 CLA (10 mol%) and 5 CAL (5 mol%) at 298 K. Simulated with ECC-lipids, SPC/E water model, ECC-ions in GROMACS 2018.0 for 1000 ns (20274 atoms). Deposited as NMRlipids Databank simulation 531 and available from https://doi.org/10.5281/zenodo.1488102. + description: Molecular dynamics trajectory of a lipid bilayer of 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 61 mol%), 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 12 mol%), + 12 SOD (12 mol%), 10 CLA (10 mol%) and 5 CAL (5 mol%) at 298 K. Simulated with + ECC-lipids, SPC/E water model, ECC-ions in GROMACS 2018.0 for 1000 ns (20274 atoms). + Deposited as NMRlipids Databank simulation 531 and available from https://doi.org/10.5281/zenodo.1488102. sameAs: https://doi.org/10.5281/zenodo.1488102 datePublished: '2018-11-14' license: @@ -158,7 +164,9 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1488102 identifier: 10.5281/zenodo.1488102 url: https://doi.org/10.5281/zenodo.1488102 - name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS (5:1) with ECC-lipids force field, and Na+ (K+) counterions at various CaCl2 additional concentrations + name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS + (5:1) with ECC-lipids force field, and Na+ (K+) counterions at various CaCl2 + additional concentrations publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/473/578/4735786c6147fb8bcf874e1c09b00b6ae73e458d/9f1edba1128d133097957c720b6f5f8c1dbee986/README.yaml b/Simulations/473/578/4735786c6147fb8bcf874e1c09b00b6ae73e458d/9f1edba1128d133097957c720b6f5f8c1dbee986/README.yaml index 16177b1bed..f4559c19d8 100644 --- a/Simulations/473/578/4735786c6147fb8bcf874e1c09b00b6ae73e458d/9f1edba1128d133097957c720b6f5f8c1dbee986/README.yaml +++ b/Simulations/473/578/4735786c6147fb8bcf874e1c09b00b6ae73e458d/9f1edba1128d133097957c720b6f5f8c1dbee986/README.yaml @@ -63,9 +63,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 287 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/POT/POPS/SOD (37:24:24:7:7) bilayer at 298 K (Lipid17 and Dang ions, GROMACS 2018.0, 1000 ns) [NMRlipids simulation 287] + name: Molecular dynamics trajectory of a POPC/CLA/POT/POPS/SOD (37:24:24:7:7) bilayer + at 298 K (Lipid17 and Dang ions, GROMACS 2018.0, 1000 ns) [NMRlipids simulation + 287] alternateName: 12POPS_60POPC_3483SOL_12SOD_39POT_39CLA_298K - description: Molecular dynamics trajectory of a lipid bilayer of 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 37 mol%), 39 CLA (24 mol%), 39 POT (24 mol%), 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 7 mol%) and 12 SOD (7 mol%) at 298 K. Simulated with Lipid17 and Dang ions in GROMACS 2018.0 for 1000 ns (20103 atoms). Deposited as NMRlipids Databank simulation 287 and available from https://doi.org/10.5281/zenodo.1487895. + description: Molecular dynamics trajectory of a lipid bilayer of 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 37 mol%), 39 CLA (24 mol%), 39 POT (24 mol%), 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, + 7 mol%) and 12 SOD (7 mol%) at 298 K. Simulated with Lipid17 and Dang ions in + GROMACS 2018.0 for 1000 ns (20103 atoms). Deposited as NMRlipids Databank simulation + 287 and available from https://doi.org/10.5281/zenodo.1487895. sameAs: https://doi.org/10.5281/zenodo.1487895 datePublished: '2018-11-14' license: @@ -158,7 +164,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1487895 identifier: 10.5281/zenodo.1487895 url: https://doi.org/10.5281/zenodo.1487895 - name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS with the lipid17 force field, NaCl and KCl salt concentrations + name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS + with the lipid17 force field, NaCl and KCl salt concentrations publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/478/b6c/478b6c725d0a406058482c7d80ee728165e4a884/d6eaf162a46bcbce0935cb07cf3927ba2f7bacbc/README.yaml b/Simulations/478/b6c/478b6c725d0a406058482c7d80ee728165e4a884/d6eaf162a46bcbce0935cb07cf3927ba2f7bacbc/README.yaml index bd7e572cfe..856f14a32e 100644 --- a/Simulations/478/b6c/478b6c725d0a406058482c7d80ee728165e4a884/d6eaf162a46bcbce0935cb07cf3927ba2f7bacbc/README.yaml +++ b/Simulations/478/b6c/478b6c725d0a406058482c7d80ee728165e4a884/d6eaf162a46bcbce0935cb07cf3927ba2f7bacbc/README.yaml @@ -53,9 +53,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 362 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (88:8:4) bilayer at 310 K (CHARMM36 NBFIX Han, GROMACS, 595 ns) [NMRlipids simulation 362] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (88:8:4) bilayer at 310 K + (CHARMM36 NBFIX Han, GROMACS, 595 ns) [NMRlipids simulation 362] alternateName: 200POPC_9000SOL_9CAL_18CLA_310K_NBFIXHan - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 88 mol%), 18 CLA (8 mol%) and 9 CAL (4 mol%) at 310 K. Simulated with CHARMM36 NBFIX Han in GROMACS for 595 ns (53827 atoms). Deposited as NMRlipids Databank simulation 362 and available from https://doi.org/10.5281/zenodo.3434396. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 88 mol%), 18 CLA (8 mol%) and 9 CAL (4 mol%) at 310 K. Simulated with CHARMM36 + NBFIX Han in GROMACS for 595 ns (53827 atoms). Deposited as NMRlipids Databank + simulation 362 and available from https://doi.org/10.5281/zenodo.3434396. sameAs: https://doi.org/10.5281/zenodo.3434396 datePublished: '2019-09-17' license: diff --git a/Simulations/479/374/47937487ddd47f9f363eed8d048e153dec3b87bd/4404adfe3d70ba3582c6bfa0656563f8eaad7887/README.yaml b/Simulations/479/374/47937487ddd47f9f363eed8d048e153dec3b87bd/4404adfe3d70ba3582c6bfa0656563f8eaad7887/README.yaml index 36497a30f3..5304663728 100644 --- a/Simulations/479/374/47937487ddd47f9f363eed8d048e153dec3b87bd/4404adfe3d70ba3582c6bfa0656563f8eaad7887/README.yaml +++ b/Simulations/479/374/47937487ddd47f9f363eed8d048e153dec3b87bd/4404adfe3d70ba3582c6bfa0656563f8eaad7887/README.yaml @@ -58,9 +58,14 @@ TEMPERATURE: 298.0 DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 178 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPG/SOD/CLA/CAL (24:24:24:18:9) bilayer at 298 K (CHARMM36, GROMACS, 300 ns) [NMRlipids simulation 178] + name: Molecular dynamics trajectory of a POPC/POPG/SOD/CLA/CAL (24:24:24:18:9) bilayer + at 298 K (CHARMM36, GROMACS, 300 ns) [NMRlipids simulation 178] alternateName: POPC:POPG(1:1)_100mMCaCl2_T298K - description: Molecular dynamics trajectory of a lipid bilayer of 150 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 24 mol%), 150 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 24 mol%), 150 SOD (24 mol%), 114 CLA (18 mol%) and 57 CAL (9 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for 300 ns (133458 atoms). Deposited as NMRlipids Databank simulation 178 and available from https://doi.org/10.5281/zenodo.4005515. + description: Molecular dynamics trajectory of a lipid bilayer of 150 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 24 mol%), 150 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 24 mol%), + 150 SOD (24 mol%), 114 CLA (18 mol%) and 57 CAL (9 mol%) at 298 K. Simulated with + CHARMM36 in GROMACS for 300 ns (133458 atoms). Deposited as NMRlipids Databank + simulation 178 and available from https://doi.org/10.5281/zenodo.4005515. sameAs: https://doi.org/10.5281/zenodo.4005515 datePublished: '2020-09-16' license: @@ -150,7 +155,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.4005515 identifier: 10.5281/zenodo.4005515 url: https://doi.org/10.5281/zenodo.4005515 - name: POPC:POPG 1:1 MD simulation with CHARMM36 in 0.1 M CaCL solution and Na+ counter ions + name: POPC:POPG 1:1 MD simulation with CHARMM36 in 0.1 M CaCL solution and Na+ + counter ions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/47b/bc6/47bbc6850bfeb294257b895017d8121a3db43510/1f6f2676b102f0c972acc567b952f3189582cdab/README.yaml b/Simulations/47b/bc6/47bbc6850bfeb294257b895017d8121a3db43510/1f6f2676b102f0c972acc567b952f3189582cdab/README.yaml index 096f80567a..8b4367c28c 100644 --- a/Simulations/47b/bc6/47bbc6850bfeb294257b895017d8121a3db43510/1f6f2676b102f0c972acc567b952f3189582cdab/README.yaml +++ b/Simulations/47b/bc6/47bbc6850bfeb294257b895017d8121a3db43510/1f6f2676b102f0c972acc567b952f3189582cdab/README.yaml @@ -51,9 +51,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 59 bioschema_properties: - name: Molecular dynamics trajectory of a CHOL/POPC (50:50) bilayer at 303 K (Berger, GROMACS Gpu-version 2020.1, 1200 ns) [NMRlipids simulation 59] + name: Molecular dynamics trajectory of a CHOL/POPC (50:50) bilayer at 303 K (Berger, + GROMACS Gpu-version 2020.1, 1200 ns) [NMRlipids simulation 59] alternateName: 256POPC_256CHOL_20480SOL_303K_Berger - description: Molecular dynamics trajectory of a lipid bilayer of 256 CHOL (cholesterol, 50 mol%) and 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 50 mol%) at 303 K. Simulated with Berger in GROMACS Gpu-version 2020.1 for 1200 ns (82176 atoms). Deposited as NMRlipids Databank simulation 59 and available from https://doi.org/10.5281/zenodo.4537794. + description: Molecular dynamics trajectory of a lipid bilayer of 256 CHOL (cholesterol, + 50 mol%) and 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 50 mol%) + at 303 K. Simulated with Berger in GROMACS Gpu-version 2020.1 for 1200 ns (82176 + atoms). Deposited as NMRlipids Databank simulation 59 and available from https://doi.org/10.5281/zenodo.4537794. sameAs: https://doi.org/10.5281/zenodo.4537794 datePublished: '2021-02-12' license: @@ -141,7 +145,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.4537794 identifier: 10.5281/zenodo.4537794 url: https://doi.org/10.5281/zenodo.4537794 - name: MD simulation of 50% POPC+50% cholesterol bilayer using Berger force field at T=303K + name: MD simulation of 50% POPC+50% cholesterol bilayer using Berger force field + at T=303K publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/47f/0a2/47f0a224270bd4c4c2da2c87b121734cbac47106/18824d047e6f5aafc6b07608c37e5ae7e7cf9e33/README.yaml b/Simulations/47f/0a2/47f0a224270bd4c4c2da2c87b121734cbac47106/18824d047e6f5aafc6b07608c37e5ae7e7cf9e33/README.yaml index 9df41cf4b4..1ae2958e55 100644 --- a/Simulations/47f/0a2/47f0a224270bd4c4c2da2c87b121734cbac47106/18824d047e6f5aafc6b07608c37e5ae7e7cf9e33/README.yaml +++ b/Simulations/47f/0a2/47f0a224270bd4c4c2da2c87b121734cbac47106/18824d047e6f5aafc6b07608c37e5ae7e7cf9e33/README.yaml @@ -52,9 +52,14 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 596 bioschema_properties: - name: Molecular dynamics trajectory of a POPE/POPG/SOD (60:20:20) bilayer at 310 K (CHARMM36 and CHARMM TIP3P, GROMACS 2018.3, 100 ns) [NMRlipids simulation 596] + name: Molecular dynamics trajectory of a POPE/POPG/SOD (60:20:20) bilayer at 310 + K (CHARMM36 and CHARMM TIP3P, GROMACS 2018.3, 100 ns) [NMRlipids simulation 596] alternateName: 126POPG_374POPE_25000SOL_126SOD_310K - description: Molecular dynamics trajectory of a lipid bilayer of 374 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 60 mol%), 126 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 20 mol%) and 126 SOD (20 mol%) at 310 K. Simulated with CHARMM36 and CHARMM TIP3P in GROMACS 2018.3 for 100 ns (137878 atoms). Deposited as NMRlipids Databank simulation 596 and available from https://doi.org/10.5281/zenodo.3249960. + description: Molecular dynamics trajectory of a lipid bilayer of 374 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, + 60 mol%), 126 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 20 mol%) + and 126 SOD (20 mol%) at 310 K. Simulated with CHARMM36 and CHARMM TIP3P in GROMACS + 2018.3 for 100 ns (137878 atoms). Deposited as NMRlipids Databank simulation 596 + and available from https://doi.org/10.5281/zenodo.3249960. sameAs: https://doi.org/10.5281/zenodo.3249960 datePublished: '2019-06-19' license: diff --git a/Simulations/47f/482/47f482884b7b15e1c51873479c951af90f05f41d/d62971dbacda12a19ca0be02ea8bb8035827b9cf/README.yaml b/Simulations/47f/482/47f482884b7b15e1c51873479c951af90f05f41d/d62971dbacda12a19ca0be02ea8bb8035827b9cf/README.yaml index 8d810a8c28..475cbfe1c1 100644 --- a/Simulations/47f/482/47f482884b7b15e1c51873479c951af90f05f41d/d62971dbacda12a19ca0be02ea8bb8035827b9cf/README.yaml +++ b/Simulations/47f/482/47f482884b7b15e1c51873479c951af90f05f41d/d62971dbacda12a19ca0be02ea8bb8035827b9cf/README.yaml @@ -40,9 +40,13 @@ EXPERIMENT: C20: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/C20 (86:14) bilayer at 333 K (SLIPIDS, GROMACS, 100 ns) [NMRlipids simulation 893] + name: Molecular dynamics trajectory of a DPPC/C20 (86:14) bilayer at 333 K (SLIPIDS, + GROMACS, 100 ns) [NMRlipids simulation 893] alternateName: DPPC/C20 - description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 86 mol%) and 12 C20 (n-Eicosane, 14 mol%) at 333 K. Simulated with SLIPIDS in GROMACS for 100 ns (13977 atoms). Deposited as NMRlipids Databank simulation 893 and available from https://doi.org/10.5281/zenodo.7572990. + description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 86 mol%) and 12 C20 (n-Eicosane, 14 mol%) at 333 K. Simulated with SLIPIDS in + GROMACS for 100 ns (13977 atoms). Deposited as NMRlipids Databank simulation 893 + and available from https://doi.org/10.5281/zenodo.7572990. sameAs: https://doi.org/10.5281/zenodo.7572990 datePublished: '2023-01-26' license: @@ -134,7 +138,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.7572990 identifier: 10.5281/zenodo.7572990 url: https://doi.org/10.5281/zenodo.7572990 - name: 'MD simulation input files and results for ,,Atomistic MD simulations of n-alkanes in a phospholipid bilayer: CHARMM36 versus Slipids"' + name: 'MD simulation input files and results for ,,Atomistic MD simulations of + n-alkanes in a phospholipid bilayer: CHARMM36 versus Slipids"' publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/483/c12/483c128ed18bf2038ea06f46aa4087d174bd7ec5/b974806c63403e6b666cfc8b0fbc2fc71bc1291f/README.yaml b/Simulations/483/c12/483c128ed18bf2038ea06f46aa4087d174bd7ec5/b974806c63403e6b666cfc8b0fbc2fc71bc1291f/README.yaml index 54ec79e70f..cd88d5c0dd 100644 --- a/Simulations/483/c12/483c128ed18bf2038ea06f46aa4087d174bd7ec5/b974806c63403e6b666cfc8b0fbc2fc71bc1291f/README.yaml +++ b/Simulations/483/c12/483c128ed18bf2038ea06f46aa4087d174bd7ec5/b974806c63403e6b666cfc8b0fbc2fc71bc1291f/README.yaml @@ -43,9 +43,12 @@ EXPERIMENT: - 10.1016/j.bbamem.2011.07.022/4 ID: 463 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC bilayer at 323 K (Slipids, GROMACS 4.6.6, 150 ns) [NMRlipids simulation 463] + name: Molecular dynamics trajectory of a DPPC bilayer at 323 K (Slipids, GROMACS + 4.6.6, 150 ns) [NMRlipids simulation 463] alternateName: 128DPPC_3840SOL_323K - description: Molecular dynamics trajectory of a lipid bilayer of 128 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) at 323 K. Simulated with Slipids in GROMACS 4.6.6 for 150 ns (28160 atoms). Deposited as NMRlipids Databank simulation 463 and available from https://doi.org/10.5281/zenodo.13287. + description: Molecular dynamics trajectory of a lipid bilayer of 128 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) + at 323 K. Simulated with Slipids in GROMACS 4.6.6 for 150 ns (28160 atoms). Deposited + as NMRlipids Databank simulation 463 and available from https://doi.org/10.5281/zenodo.13287. sameAs: https://doi.org/10.5281/zenodo.13287 datePublished: '2014-12-17' license: diff --git a/Simulations/488/3d3/4883d3f18b4a39d46ed8c55918b726d0af5d5642/49c77f52881d765017002fe00fc6b28c470b2433/README.yaml b/Simulations/488/3d3/4883d3f18b4a39d46ed8c55918b726d0af5d5642/49c77f52881d765017002fe00fc6b28c470b2433/README.yaml index 84c49e0ac4..092a88acbd 100644 --- a/Simulations/488/3d3/4883d3f18b4a39d46ed8c55918b726d0af5d5642/49c77f52881d765017002fe00fc6b28c470b2433/README.yaml +++ b/Simulations/488/3d3/4883d3f18b4a39d46ed8c55918b726d0af5d5642/49c77f52881d765017002fe00fc6b28c470b2433/README.yaml @@ -44,9 +44,12 @@ EXPERIMENT: DRPC: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a DRPC bilayer at 333.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 633] + name: Molecular dynamics trajectory of a DRPC bilayer at 333.15 K (CHARMM36, GROMACS, + 1001 ns) [NMRlipids simulation 633] alternateName: 1024DRPC_51200SOL_333K - description: Molecular dynamics trajectory of a lipid bilayer of 1024 DRPC (1,2-(14:1$^\Delta9$)-sn-glycero-3-phosphocholine) at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (270336 atoms). Deposited as NMRlipids Databank simulation 633 and available from https://doi.org/10.5281/zenodo.6943413. + description: Molecular dynamics trajectory of a lipid bilayer of 1024 DRPC (1,2-(14:1$^\Delta9$)-sn-glycero-3-phosphocholine) + at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (270336 atoms). Deposited + as NMRlipids Databank simulation 633 and available from https://doi.org/10.5281/zenodo.6943413. sameAs: https://doi.org/10.5281/zenodo.6943413 datePublished: '2022-07-30' license: @@ -134,7 +137,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.6943413 identifier: 10.5281/zenodo.6943413 url: https://doi.org/10.5281/zenodo.6943413 - name: Simulations of different single-component bilayers, three different system sizes + name: Simulations of different single-component bilayers, three different system + sizes publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/48c/f67/48cf67cc732e80a1e8eac1161d32017e04160e4a/0513321b85277383f208ae5655856fd3ffb47333/README.yaml b/Simulations/48c/f67/48cf67cc732e80a1e8eac1161d32017e04160e4a/0513321b85277383f208ae5655856fd3ffb47333/README.yaml index 39f4449c2a..a73a4314cf 100644 --- a/Simulations/48c/f67/48cf67cc732e80a1e8eac1161d32017e04160e4a/0513321b85277383f208ae5655856fd3ffb47333/README.yaml +++ b/Simulations/48c/f67/48cf67cc732e80a1e8eac1161d32017e04160e4a/0513321b85277383f208ae5655856fd3ffb47333/README.yaml @@ -55,9 +55,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 868 bioschema_properties: - name: Molecular dynamics trajectory of a NH4/POPI/POPC (38:38:25) bilayer at 310 K (CHARMM36, GROMACS 2022.4, 500 ns) [NMRlipids simulation 868] + name: Molecular dynamics trajectory of a NH4/POPI/POPC (38:38:25) bilayer at 310 + K (CHARMM36, GROMACS 2022.4, 500 ns) [NMRlipids simulation 868] alternateName: POPI-POPC (60:40), full hydration, 310 K, NH4+ counter ions - description: Molecular dynamics trajectory of a lipid bilayer of 120 NH4 (38 mol%), 120 POPI (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoinositol, 38 mol%) and 80 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 25 mol%) at 310 K. Simulated with CHARMM36 in GROMACS 2022.4 for 500 ns (57760 atoms). Deposited as NMRlipids Databank simulation 868 and available from https://doi.org/10.5281/zenodo.10254558. + description: Molecular dynamics trajectory of a lipid bilayer of 120 NH4 (38 mol%), + 120 POPI (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoinositol, 38 mol%) and 80 POPC + (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 25 mol%) at 310 K. Simulated + with CHARMM36 in GROMACS 2022.4 for 500 ns (57760 atoms). Deposited as NMRlipids + Databank simulation 868 and available from https://doi.org/10.5281/zenodo.10254558. sameAs: https://doi.org/10.5281/zenodo.10254558 datePublished: '2023-12-18' license: diff --git a/Simulations/492/100/492100cdfee39e4b427f1f4563c635839b40c2a4/b14f6e506122f9754896c3edb69f0fa9075272fb/README.yaml b/Simulations/492/100/492100cdfee39e4b427f1f4563c635839b40c2a4/b14f6e506122f9754896c3edb69f0fa9075272fb/README.yaml index 6a1eb5e0d9..6ae51a6e96 100644 --- a/Simulations/492/100/492100cdfee39e4b427f1f4563c635839b40c2a4/b14f6e506122f9754896c3edb69f0fa9075272fb/README.yaml +++ b/Simulations/492/100/492100cdfee39e4b427f1f4563c635839b40c2a4/b14f6e506122f9754896c3edb69f0fa9075272fb/README.yaml @@ -50,9 +50,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/5 ID: 691 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (80:20) bilayer at 298.15 K (Slipids, GROMACS 2021, 1001 ns) [NMRlipids simulation 691] + name: Molecular dynamics trajectory of a POPC/CHOL (80:20) bilayer at 298.15 K (Slipids, + GROMACS 2021, 1001 ns) [NMRlipids simulation 691] alternateName: Slipids_POPC_CHOL20_L - description: Molecular dynamics trajectory of a lipid bilayer of 1024 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 80 mol%) and 256 CHOL (cholesterol, 20 mol%) at 298.15 K. Simulated with Slipids in GROMACS 2021 for 1001 ns (348160 atoms). Deposited as NMRlipids Databank simulation 691 and available from https://doi.org/10.5281/zenodo.7022749. + description: Molecular dynamics trajectory of a lipid bilayer of 1024 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 80 mol%) and 256 CHOL (cholesterol, 20 mol%) at 298.15 K. Simulated with Slipids + in GROMACS 2021 for 1001 ns (348160 atoms). Deposited as NMRlipids Databank simulation + 691 and available from https://doi.org/10.5281/zenodo.7022749. sameAs: https://doi.org/10.5281/zenodo.7022749 datePublished: '2022-08-23' license: diff --git a/Simulations/498/85f/49885ff5bdaa1472e8f6375abc64fe3fdb42ab4d/7bbc5b902e5874b3e1db04a8aad3bd79dfe2b714/README.yaml b/Simulations/498/85f/49885ff5bdaa1472e8f6375abc64fe3fdb42ab4d/7bbc5b902e5874b3e1db04a8aad3bd79dfe2b714/README.yaml index bba23c50f2..21234db083 100644 --- a/Simulations/498/85f/49885ff5bdaa1472e8f6375abc64fe3fdb42ab4d/7bbc5b902e5874b3e1db04a8aad3bd79dfe2b714/README.yaml +++ b/Simulations/498/85f/49885ff5bdaa1472e8f6375abc64fe3fdb42ab4d/7bbc5b902e5874b3e1db04a8aad3bd79dfe2b714/README.yaml @@ -51,9 +51,13 @@ EXPERIMENT: POPC: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (79:14:7) bilayer at 310 K (CHARMM36, GROMACS 2022.5-plumed_2.8.2, 1000 ns) [NMRlipids simulation 923] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (79:14:7) bilayer at 310 K + (CHARMM36, GROMACS 2022.5-plumed_2.8.2, 1000 ns) [NMRlipids simulation 923] alternateName: POPC bilayer at 310K with the CHARMM36 force field, 111 mM CaCl2 - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 79 mol%), 36 CLA (14 mol%) and 18 CAL (7 mol%) at 310 K. Simulated with CHARMM36 in GROMACS 2022.5-plumed_2.8.2 for 1000 ns (53854 atoms). Deposited as NMRlipids Databank simulation 923 and available from https://doi.org/10.5281/zenodo.10464498. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 79 mol%), 36 CLA (14 mol%) and 18 CAL (7 mol%) at 310 K. Simulated with CHARMM36 + in GROMACS 2022.5-plumed_2.8.2 for 1000 ns (53854 atoms). Deposited as NMRlipids + Databank simulation 923 and available from https://doi.org/10.5281/zenodo.10464498. sameAs: https://doi.org/10.5281/zenodo.10464498 datePublished: '2024-01-06' license: @@ -150,4 +154,4 @@ bioschema_properties: api: datacite doi: 10.5281/zenodo.10464498 spdxLicenseList: 3.28.0 - retrieved: '2026-09-09' \ No newline at end of file + retrieved: '2026-09-09' diff --git a/Simulations/49b/2a9/49b2a928e2ac964a8b1ccf3051ce1138aaf0f09a/afa6ce0d88b97ba152eb31af522ca061adb31876/README.yaml b/Simulations/49b/2a9/49b2a928e2ac964a8b1ccf3051ce1138aaf0f09a/afa6ce0d88b97ba152eb31af522ca061adb31876/README.yaml index 38bfe17207..4297867e27 100644 --- a/Simulations/49b/2a9/49b2a928e2ac964a8b1ccf3051ce1138aaf0f09a/afa6ce0d88b97ba152eb31af522ca061adb31876/README.yaml +++ b/Simulations/49b/2a9/49b2a928e2ac964a8b1ccf3051ce1138aaf0f09a/afa6ce0d88b97ba152eb31af522ca061adb31876/README.yaml @@ -46,9 +46,12 @@ EXPERIMENT: - 10.1016/j.bbamem.2011.07.022/10 ID: 27 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC bilayer at 333.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 27] + name: Molecular dynamics trajectory of a DPPC bilayer at 333.15 K (CHARMM36, GROMACS, + 1001 ns) [NMRlipids simulation 27] alternateName: 64DPPC_3200SOL_333K - description: Molecular dynamics trajectory of a lipid bilayer of 64 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (17920 atoms). Deposited as NMRlipids Databank simulation 27 and available from https://doi.org/10.5281/zenodo.6943413. + description: Molecular dynamics trajectory of a lipid bilayer of 64 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) + at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (17920 atoms). Deposited + as NMRlipids Databank simulation 27 and available from https://doi.org/10.5281/zenodo.6943413. sameAs: https://doi.org/10.5281/zenodo.6943413 datePublished: '2022-07-30' license: @@ -139,7 +142,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.6943413 identifier: 10.5281/zenodo.6943413 url: https://doi.org/10.5281/zenodo.6943413 - name: Simulations of different single-component bilayers, three different system sizes + name: Simulations of different single-component bilayers, three different system + sizes publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/49d/6ce/49d6cefb7e4c1b186ac65c40414c69ef572a62b8/91b0cb04ece782a635633afefdb3950963e9c4a5/README.yaml b/Simulations/49d/6ce/49d6cefb7e4c1b186ac65c40414c69ef572a62b8/91b0cb04ece782a635633afefdb3950963e9c4a5/README.yaml index b8dd98dffa..ae8df8e255 100644 --- a/Simulations/49d/6ce/49d6cefb7e4c1b186ac65c40414c69ef572a62b8/91b0cb04ece782a635633afefdb3950963e9c4a5/README.yaml +++ b/Simulations/49d/6ce/49d6cefb7e4c1b186ac65c40414c69ef572a62b8/91b0cb04ece782a635633afefdb3950963e9c4a5/README.yaml @@ -49,9 +49,15 @@ SOFTWARE: gromacs DIR_WRK: /usr/home/bort/Databank ID: 122 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (48:35:17) bilayer at 310 K (Slipids for lipids, amber for CaCl_2 (default amber ion parameters type C0), GROMACS, 100 ns) [NMRlipids simulation 122] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (48:35:17) bilayer at 310 + K (Slipids for lipids, amber for CaCl_2 (default amber ion parameters type C0), + GROMACS, 100 ns) [NMRlipids simulation 122] alternateName: 200POPC_9000SOL_73CAL_146CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 48 mol%), 146 CLA (35 mol%) and 73 CAL (17 mol%) at 310 K. Simulated with Slipids for lipids, amber for CaCl_2 (default amber ion parameters type C0) in GROMACS for 100 ns (54019 atoms). Deposited as NMRlipids Databank simulation 122 and available from https://doi.org/10.5281/zenodo.51182. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 48 mol%), 146 CLA (35 mol%) and 73 CAL (17 mol%) at 310 K. Simulated with Slipids + for lipids, amber for CaCl_2 (default amber ion parameters type C0) in GROMACS + for 100 ns (54019 atoms). Deposited as NMRlipids Databank simulation 122 and available + from https://doi.org/10.5281/zenodo.51182. sameAs: https://doi.org/10.5281/zenodo.51182 datePublished: '2016-05-09' license: @@ -99,7 +105,8 @@ bioschema_properties: inDefinedTermSet: http://edamontology.org url: http://edamontology.org/operation_2476 - Molecular dynamics simulation (gromacs) - - Slipids for lipids, amber for CaCl_2 (default amber ion parameters type C0) force field + - Slipids for lipids, amber for CaCl_2 (default amber ion parameters type C0) force + field variableMeasured: - '@type': PropertyValue name: area per lipid diff --git a/Simulations/49d/6ce/49d6cefb7e4c1b186ac65c40414c69ef572a62b8/a08afcbbe31cf7c4569f4eae864e0e915efed0ad/README.yaml b/Simulations/49d/6ce/49d6cefb7e4c1b186ac65c40414c69ef572a62b8/a08afcbbe31cf7c4569f4eae864e0e915efed0ad/README.yaml index bd5c1251e4..ba2b660070 100644 --- a/Simulations/49d/6ce/49d6cefb7e4c1b186ac65c40414c69ef572a62b8/a08afcbbe31cf7c4569f4eae864e0e915efed0ad/README.yaml +++ b/Simulations/49d/6ce/49d6cefb7e4c1b186ac65c40414c69ef572a62b8/a08afcbbe31cf7c4569f4eae864e0e915efed0ad/README.yaml @@ -50,9 +50,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 121 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (48:35:17) bilayer at 310 K (Slipids with default Amber ions parameters (type C0), GROMACS 4.6, 2000 ns) [NMRlipids simulation 121] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (48:35:17) bilayer at 310 + K (Slipids with default Amber ions parameters (type C0), GROMACS 4.6, 2000 ns) + [NMRlipids simulation 121] alternateName: 200POPC_9000SOL_73CAL_146CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 48 mol%), 146 CLA (35 mol%) and 73 CAL (17 mol%) at 310 K. Simulated with Slipids with default Amber ions parameters (type C0) in GROMACS 4.6 for 2000 ns (54019 atoms). Deposited as NMRlipids Databank simulation 121 and available from https://doi.org/10.5281/zenodo.259349. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 48 mol%), 146 CLA (35 mol%) and 73 CAL (17 mol%) at 310 K. Simulated with Slipids + with default Amber ions parameters (type C0) in GROMACS 4.6 for 2000 ns (54019 + atoms). Deposited as NMRlipids Databank simulation 121 and available from https://doi.org/10.5281/zenodo.259349. sameAs: https://doi.org/10.5281/zenodo.259349 datePublished: '2017-01-24' license: @@ -140,7 +145,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.259349 identifier: 10.5281/zenodo.259349 url: https://doi.org/10.5281/zenodo.259349 - name: Popc With Varying Amounts Of Cholesterol, 450 Mm Of Cacl_2. Slipids With Default Amber Ions + name: Popc With Varying Amounts Of Cholesterol, 450 Mm Of Cacl_2. Slipids With + Default Amber Ions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/4ab/f43/4abf4377e806bf68d35bb298a5eeb98fde0d8753/fb3a01cc92a2d21c327eccd1b4a8f3f99586e972/README.yaml b/Simulations/4ab/f43/4abf4377e806bf68d35bb298a5eeb98fde0d8753/fb3a01cc92a2d21c327eccd1b4a8f3f99586e972/README.yaml index 17dad17960..5ca503e599 100644 --- a/Simulations/4ab/f43/4abf4377e806bf68d35bb298a5eeb98fde0d8753/fb3a01cc92a2d21c327eccd1b4a8f3f99586e972/README.yaml +++ b/Simulations/4ab/f43/4abf4377e806bf68d35bb298a5eeb98fde0d8753/fb3a01cc92a2d21c327eccd1b4a8f3f99586e972/README.yaml @@ -58,9 +58,15 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 210 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL/CHOL (45:33:17:5) bilayer at 310.15 K (CHARMM36 with incorrect multiplicity in dihedrals and ECC ions, GROMACS 5.0, 800 ns) [NMRlipids simulation 210] + name: Molecular dynamics trajectory of a POPC/CLA/CAL/CHOL (45:33:17:5) bilayer + at 310.15 K (CHARMM36 with incorrect multiplicity in dihedrals and ECC ions, GROMACS + 5.0, 800 ns) [NMRlipids simulation 210] alternateName: 22CHOL_200POPC_9000SOL_73CAL_146CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 45 mol%), 146 CLA (33 mol%), 73 CAL (17 mol%) and 22 CHOL (cholesterol, 5 mol%) at 310.15 K. Simulated with CHARMM36 with incorrect multiplicity in dihedrals and ECC ions in GROMACS 5.0 for 800 ns (55647 atoms). Deposited as NMRlipids Databank simulation 210 and available from https://doi.org/10.5281/zenodo.259376. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 45 mol%), 146 CLA (33 mol%), 73 CAL (17 mol%) and 22 CHOL (cholesterol, 5 mol%) + at 310.15 K. Simulated with CHARMM36 with incorrect multiplicity in dihedrals + and ECC ions in GROMACS 5.0 for 800 ns (55647 atoms). Deposited as NMRlipids Databank + simulation 210 and available from https://doi.org/10.5281/zenodo.259376. sameAs: https://doi.org/10.5281/zenodo.259376 datePublished: '2017-01-24' license: @@ -150,7 +156,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.259376 identifier: 10.5281/zenodo.259376 url: https://doi.org/10.5281/zenodo.259376 - name: Popc With Varying Amounts Of Cholesterol, 450 Mm Of Cacl_2. Charmm36 With Ecc-Scaled Ions + name: Popc With Varying Amounts Of Cholesterol, 450 Mm Of Cacl_2. Charmm36 With + Ecc-Scaled Ions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/4ac/992/4ac992db0dadcc3bfb0df27ebf251b90f5baa149/015d190ed68b0e1786e40811df5a9c4501ce977b/README.yaml b/Simulations/4ac/992/4ac992db0dadcc3bfb0df27ebf251b90f5baa149/015d190ed68b0e1786e40811df5a9c4501ce977b/README.yaml index 2bc0259f1f..3876290020 100644 --- a/Simulations/4ac/992/4ac992db0dadcc3bfb0df27ebf251b90f5baa149/015d190ed68b0e1786e40811df5a9c4501ce977b/README.yaml +++ b/Simulations/4ac/992/4ac992db0dadcc3bfb0df27ebf251b90f5baa149/015d190ed68b0e1786e40811df5a9c4501ce977b/README.yaml @@ -62,9 +62,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 844 bioschema_properties: - name: Molecular dynamics trajectory of a PYPE/POT/DOPG/CLA/PVCL (47:28:13:9:3) bilayer at 310 K (CHARMM36, GROMACS 2023+, 1000 ns) [NMRlipids simulation 844] + name: Molecular dynamics trajectory of a PYPE/POT/DOPG/CLA/PVCL (47:28:13:9:3) bilayer + at 310 K (CHARMM36, GROMACS 2023+, 1000 ns) [NMRlipids simulation 844] alternateName: ECOLI_MODEL_MEMBRANE_UIB - description: Molecular dynamics trajectory of a lipid bilayer of 150 PYPE (1-(16:0)-2-(16:1$^\Delta9$)-sn-glycero-3-phosphoethanolamine, 47 mol%), 88 POT (28 mol%), 40 DOPG (1,2-dioleoyl-sn-glycero-3-phosphoglycerol, 13 mol%), 28 CLA (9 mol%) and 10 PVCL (1',3'-bis-[1-hexadecanoyl-2-(11Z-octadecenoyl)-sn-glycero-3-phospho]-sn-glycerol, 3 mol%) at 310 K. Simulated with CHARMM36 in GROMACS 2023+ for 1000 ns (58594 atoms). Deposited as NMRlipids Databank simulation 844 and available from https://doi.org/10.5281/zenodo.16842791. + description: Molecular dynamics trajectory of a lipid bilayer of 150 PYPE (1-(16:0)-2-(16:1$^\Delta9$)-sn-glycero-3-phosphoethanolamine, + 47 mol%), 88 POT (28 mol%), 40 DOPG (1,2-dioleoyl-sn-glycero-3-phosphoglycerol, + 13 mol%), 28 CLA (9 mol%) and 10 PVCL (1',3'-bis-[1-hexadecanoyl-2-(11Z-octadecenoyl)-sn-glycero-3-phospho]-sn-glycerol, + 3 mol%) at 310 K. Simulated with CHARMM36 in GROMACS 2023+ for 1000 ns (58594 + atoms). Deposited as NMRlipids Databank simulation 844 and available from https://doi.org/10.5281/zenodo.16842791. sameAs: https://doi.org/10.5281/zenodo.16842791 datePublished: '2025-08-13' license: diff --git a/Simulations/4ad/86c/4ad86cb9b8971f9acb7697e534c919359c720f91/5021b8fd43b9f7147ed1d883c1ccc172da878160/README.yaml b/Simulations/4ad/86c/4ad86cb9b8971f9acb7697e534c919359c720f91/5021b8fd43b9f7147ed1d883c1ccc172da878160/README.yaml index a696d3d767..399323c023 100644 --- a/Simulations/4ad/86c/4ad86cb9b8971f9acb7697e534c919359c720f91/5021b8fd43b9f7147ed1d883c1ccc172da878160/README.yaml +++ b/Simulations/4ad/86c/4ad86cb9b8971f9acb7697e534c919359c720f91/5021b8fd43b9f7147ed1d883c1ccc172da878160/README.yaml @@ -41,9 +41,12 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 537 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC bilayer at 358 K (CHARMM36, GROMACS 2016.4, 49 ns) [NMRlipids simulation 537] + name: Molecular dynamics trajectory of a DPPC bilayer at 358 K (CHARMM36, GROMACS + 2016.4, 49 ns) [NMRlipids simulation 537] alternateName: 212DPPC_29826SOL_358K - description: Molecular dynamics trajectory of a lipid bilayer of 212 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) at 358 K. Simulated with CHARMM36 in GROMACS 2016.4 for 49 ns (117038 atoms). Deposited as NMRlipids Databank simulation 537 and available from https://doi.org/10.5281/zenodo.3950029. + description: Molecular dynamics trajectory of a lipid bilayer of 212 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) + at 358 K. Simulated with CHARMM36 in GROMACS 2016.4 for 49 ns (117038 atoms). + Deposited as NMRlipids Databank simulation 537 and available from https://doi.org/10.5281/zenodo.3950029. sameAs: https://doi.org/10.5281/zenodo.3950029 datePublished: '2020-07-20' license: @@ -143,7 +146,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3950029 identifier: 10.5281/zenodo.3950029 url: https://doi.org/10.5281/zenodo.3950029 - name: 212 DPPC Molecules bilayer in pure Water, simulated at temperatures ranging from 288K to 358K + name: 212 DPPC Molecules bilayer in pure Water, simulated at temperatures ranging + from 288K to 358K publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/4ad/924/4ad924312f0e7b81a0d32ddaca8e45e12c07cb5d/10c6f1a141639edda350ff24018a53bb164f8d48/README.yaml b/Simulations/4ad/924/4ad924312f0e7b81a0d32ddaca8e45e12c07cb5d/10c6f1a141639edda350ff24018a53bb164f8d48/README.yaml index 9ddab920f7..1e93fed9fa 100644 --- a/Simulations/4ad/924/4ad924312f0e7b81a0d32ddaca8e45e12c07cb5d/10c6f1a141639edda350ff24018a53bb164f8d48/README.yaml +++ b/Simulations/4ad/924/4ad924312f0e7b81a0d32ddaca8e45e12c07cb5d/10c6f1a141639edda350ff24018a53bb164f8d48/README.yaml @@ -55,9 +55,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 536 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/CLA/SOD (41:29:29) bilayer at 323 K (Berger-DPPC-98, GROMACS 5.0.4, 120 ns) [NMRlipids simulation 536] + name: Molecular dynamics trajectory of a DPPC/CLA/SOD (41:29:29) bilayer at 323 + K (Berger-DPPC-98, GROMACS 5.0.4, 120 ns) [NMRlipids simulation 536] alternateName: 72DPPC_2778SOL_51SOD_51CLA_323K - description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 41 mol%), 51 CLA (29 mol%) and 51 SOD (29 mol%) at 323 K. Simulated with Berger-DPPC-98 in GROMACS 5.0.4 for 120 ns (12036 atoms). Deposited as NMRlipids Databank simulation 536 and available from https://doi.org/10.5281/zenodo.17228. + description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 41 mol%), 51 CLA (29 mol%) and 51 SOD (29 mol%) at 323 K. Simulated with Berger-DPPC-98 + in GROMACS 5.0.4 for 120 ns (12036 atoms). Deposited as NMRlipids Databank simulation + 536 and available from https://doi.org/10.5281/zenodo.17228. sameAs: https://doi.org/10.5281/zenodo.17228 datePublished: '2015-04-29' license: diff --git a/Simulations/4b3/86c/4b386cc498c5e540aa44e2123fa4720afc544428/a0c82b1035ff5fdbf8d443b90404ddeb3365d924/README.yaml b/Simulations/4b3/86c/4b386cc498c5e540aa44e2123fa4720afc544428/a0c82b1035ff5fdbf8d443b90404ddeb3365d924/README.yaml index 0e89e2fa19..c49f51d169 100644 --- a/Simulations/4b3/86c/4b386cc498c5e540aa44e2123fa4720afc544428/a0c82b1035ff5fdbf8d443b90404ddeb3365d924/README.yaml +++ b/Simulations/4b3/86c/4b386cc498c5e540aa44e2123fa4720afc544428/a0c82b1035ff5fdbf8d443b90404ddeb3365d924/README.yaml @@ -50,9 +50,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/5 ID: 692 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (80:20) bilayer at 298.15 K (Slipids, GROMACS 2021, 1001 ns) [NMRlipids simulation 692] + name: Molecular dynamics trajectory of a POPC/CHOL (80:20) bilayer at 298.15 K (Slipids, + GROMACS 2021, 1001 ns) [NMRlipids simulation 692] alternateName: Slipids_POPC_CHOL20_S - description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 80 mol%) and 16 CHOL (cholesterol, 20 mol%) at 298.15 K. Simulated with Slipids in GROMACS 2021 for 1001 ns (21760 atoms). Deposited as NMRlipids Databank simulation 692 and available from https://doi.org/10.5281/zenodo.7022749. + description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 80 mol%) and 16 CHOL (cholesterol, 20 mol%) at 298.15 K. Simulated with Slipids + in GROMACS 2021 for 1001 ns (21760 atoms). Deposited as NMRlipids Databank simulation + 692 and available from https://doi.org/10.5281/zenodo.7022749. sameAs: https://doi.org/10.5281/zenodo.7022749 datePublished: '2022-08-23' license: diff --git a/Simulations/4ba/6f1/4ba6f1d4240b72a165d921ec0246b14167ceeb9e/4ba6f1d4240b72a165d921ec0246b14167ceeb9e/README.yaml b/Simulations/4ba/6f1/4ba6f1d4240b72a165d921ec0246b14167ceeb9e/4ba6f1d4240b72a165d921ec0246b14167ceeb9e/README.yaml index 6bf407e72c..49ceb95bcd 100644 --- a/Simulations/4ba/6f1/4ba6f1d4240b72a165d921ec0246b14167ceeb9e/4ba6f1d4240b72a165d921ec0246b14167ceeb9e/README.yaml +++ b/Simulations/4ba/6f1/4ba6f1d4240b72a165d921ec0246b14167ceeb9e/4ba6f1d4240b72a165d921ec0246b14167ceeb9e/README.yaml @@ -46,9 +46,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 740 bioschema_properties: - name: Molecular dynamics trajectory of a DOPC/CLA/SOD (51:25:25) bilayer at 303 K (AMOEBA, OPENMM v7.5.1, 202 ns) [NMRlipids simulation 740] + name: Molecular dynamics trajectory of a DOPC/CLA/SOD (51:25:25) bilayer at 303 + K (AMOEBA, OPENMM v7.5.1, 202 ns) [NMRlipids simulation 740] alternateName: DOPC_1000mM_NaCl_at_303K_with_AMOEBA - description: Molecular dynamics trajectory of a lipid bilayer of 72 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, 51 mol%), 35 CLA (25 mol%) and 35 SOD (25 mol%) at 303 K. Simulated with AMOEBA in OPENMM v7.5.1 for 202 ns (18646 atoms). Deposited as NMRlipids Databank simulation 740 and available from https://doi.org/10.5281/zenodo.7625844. + description: Molecular dynamics trajectory of a lipid bilayer of 72 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, + 51 mol%), 35 CLA (25 mol%) and 35 SOD (25 mol%) at 303 K. Simulated with AMOEBA + in OPENMM v7.5.1 for 202 ns (18646 atoms). Deposited as NMRlipids Databank simulation + 740 and available from https://doi.org/10.5281/zenodo.7625844. sameAs: https://doi.org/10.5281/zenodo.7625844 datePublished: '2023-02-09' license: @@ -136,7 +140,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.7625844 identifier: 10.5281/zenodo.7625844 url: https://doi.org/10.5281/zenodo.7625844 - name: MD Simulation data for a pure DOPC bilayer (1000 mM NaCl) with AMOEBA force field + OpenMM + name: MD Simulation data for a pure DOPC bilayer (1000 mM NaCl) with AMOEBA force + field + OpenMM publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/4c0/a5a/4c0a5a56fa8bf3206b53d7f036e1785f99ee12b2/0096be1477092d8c53aadb8dc86cc18584c9f4a3/README.yaml b/Simulations/4c0/a5a/4c0a5a56fa8bf3206b53d7f036e1785f99ee12b2/0096be1477092d8c53aadb8dc86cc18584c9f4a3/README.yaml index ba36ee2283..3b6fe85240 100644 --- a/Simulations/4c0/a5a/4c0a5a56fa8bf3206b53d7f036e1785f99ee12b2/0096be1477092d8c53aadb8dc86cc18584c9f4a3/README.yaml +++ b/Simulations/4c0/a5a/4c0a5a56fa8bf3206b53d7f036e1785f99ee12b2/0096be1477092d8c53aadb8dc86cc18584c9f4a3/README.yaml @@ -44,9 +44,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 815 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 300 K (OPLS3e, GROMACS 2019-4, 490 ns) [NMRlipids simulation 815] + name: Molecular dynamics trajectory of a POPC bilayer at 300 K (OPLS3e, GROMACS + 2019-4, 490 ns) [NMRlipids simulation 815] alternateName: 200POPC_4kSOL_300K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 300 K. Simulated with OPLS3e in GROMACS 2019-4 for 490 ns (38800 atoms). Deposited as NMRlipids Databank simulation 815 and available from https://doi.org/10.5281/zenodo.10183802. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 300 K. Simulated with OPLS3e in GROMACS 2019-4 for 490 ns (38800 atoms). Deposited + as NMRlipids Databank simulation 815 and available from https://doi.org/10.5281/zenodo.10183802. sameAs: https://doi.org/10.5281/zenodo.10183802 datePublished: '2022' license: diff --git a/Simulations/4c9/974/4c9974b6ffddd41804871d212606f70bad95e1c1/ea8241cd4cad7248409dd67a72f63a8a0f8ba35a/README.yaml b/Simulations/4c9/974/4c9974b6ffddd41804871d212606f70bad95e1c1/ea8241cd4cad7248409dd67a72f63a8a0f8ba35a/README.yaml index a1327307ec..a055ead4f9 100644 --- a/Simulations/4c9/974/4c9974b6ffddd41804871d212606f70bad95e1c1/ea8241cd4cad7248409dd67a72f63a8a0f8ba35a/README.yaml +++ b/Simulations/4c9/974/4c9974b6ffddd41804871d212606f70bad95e1c1/ea8241cd4cad7248409dd67a72f63a8a0f8ba35a/README.yaml @@ -55,9 +55,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 444 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (84:8:8) bilayer at 298.15 K (Ulmschneider, GROMACS 5.0.3, 200 ns) [NMRlipids simulation 444] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (84:8:8) bilayer at 298.15 + K (Ulmschneider, GROMACS 5.0.3, 200 ns) [NMRlipids simulation 444] alternateName: 128POPC_5120SOL_12SOD_12CLA_298K - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 84 mol%), 12 CLA (8 mol%) and 12 SOD (8 mol%) at 298.15 K. Simulated with Ulmschneider in GROMACS 5.0.3 for 200 ns (22040 atoms). Deposited as NMRlipids Databank simulation 444 and available from https://doi.org/10.5281/zenodo.30892. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 84 mol%), 12 CLA (8 mol%) and 12 SOD (8 mol%) at 298.15 K. Simulated with Ulmschneider + in GROMACS 5.0.3 for 200 ns (22040 atoms). Deposited as NMRlipids Databank simulation + 444 and available from https://doi.org/10.5281/zenodo.30892. sameAs: https://doi.org/10.5281/zenodo.30892 datePublished: '2015-09-11' license: diff --git a/Simulations/4cd/ebe/4cdebe389bf43596e93cd717a876a04785ae0f46/d8b3fa421e3d820164356617e705e685c70cbb73/README.yaml b/Simulations/4cd/ebe/4cdebe389bf43596e93cd717a876a04785ae0f46/d8b3fa421e3d820164356617e705e685c70cbb73/README.yaml index ffede0f183..1c24cc75d7 100644 --- a/Simulations/4cd/ebe/4cdebe389bf43596e93cd717a876a04785ae0f46/d8b3fa421e3d820164356617e705e685c70cbb73/README.yaml +++ b/Simulations/4cd/ebe/4cdebe389bf43596e93cd717a876a04785ae0f46/d8b3fa421e3d820164356617e705e685c70cbb73/README.yaml @@ -62,9 +62,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 465 bioschema_properties: - name: Molecular dynamics trajectory of a SOD/CLA/POPC/POPS (39:34:22:4) bilayer at 298 K (ECC-lipids, GROMACS 2018.0, 1000 ns) [NMRlipids simulation 465] + name: Molecular dynamics trajectory of a SOD/CLA/POPC/POPS (39:34:22:4) bilayer + at 298 K (ECC-lipids, GROMACS 2018.0, 1000 ns) [NMRlipids simulation 465] alternateName: 12POPS_60POPC_3377SOL_104SOD_92CLA_298K - description: Molecular dynamics trajectory of a lipid bilayer of 104 SOD (39 mol%), 92 CLA (34 mol%), 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 22 mol%) and 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 4 mol%) at 298 K. Simulated with ECC-lipids in GROMACS 2018.0 for 1000 ns (19891 atoms). Deposited as NMRlipids Databank simulation 465 and available from https://doi.org/10.5281/zenodo.3332778. + description: Molecular dynamics trajectory of a lipid bilayer of 104 SOD (39 mol%), + 92 CLA (34 mol%), 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 22 + mol%) and 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 4 mol%) + at 298 K. Simulated with ECC-lipids in GROMACS 2018.0 for 1000 ns (19891 atoms). + Deposited as NMRlipids Databank simulation 465 and available from https://doi.org/10.5281/zenodo.3332778. sameAs: https://doi.org/10.5281/zenodo.3332778 datePublished: '2018-11-14' license: @@ -156,7 +161,9 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3332778 identifier: 10.5281/zenodo.3332778 url: https://doi.org/10.5281/zenodo.3332778 - name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS (5:1) with ECC-lipids force field, and Na+ (K+) counterions at various additional concentrations of NaCl and KCl + name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS + (5:1) with ECC-lipids force field, and Na+ (K+) counterions at various additional + concentrations of NaCl and KCl publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/4d9/88b/4d988baf4bd19a0b0c1580c1869da7f69f9ae214/02793139a49ab512c67031fd1e7cad7668fa9117/README.yaml b/Simulations/4d9/88b/4d988baf4bd19a0b0c1580c1869da7f69f9ae214/02793139a49ab512c67031fd1e7cad7668fa9117/README.yaml index e3ce470188..902848be4e 100644 --- a/Simulations/4d9/88b/4d988baf4bd19a0b0c1580c1869da7f69f9ae214/02793139a49ab512c67031fd1e7cad7668fa9117/README.yaml +++ b/Simulations/4d9/88b/4d988baf4bd19a0b0c1580c1869da7f69f9ae214/02793139a49ab512c67031fd1e7cad7668fa9117/README.yaml @@ -48,9 +48,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 874 bioschema_properties: - name: Molecular dynamics trajectory of a NH4/POPI (50:50) bilayer at 310 K (CHARMM36, GROMACS 2022.4, 500 ns) [NMRlipids simulation 874] + name: Molecular dynamics trajectory of a NH4/POPI (50:50) bilayer at 310 K (CHARMM36, + GROMACS 2022.4, 500 ns) [NMRlipids simulation 874] alternateName: POPI, full hydration, 310 K, NH4+ counter ions - description: Molecular dynamics trajectory of a lipid bilayer of 200 NH4 (50 mol%) and 200 POPI (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoinositol, 50 mol%) at 310 K. Simulated with CHARMM36 in GROMACS 2022.4 for 500 ns (58400 atoms). Deposited as NMRlipids Databank simulation 874 and available from https://doi.org/10.5281/zenodo.10242899. + description: Molecular dynamics trajectory of a lipid bilayer of 200 NH4 (50 mol%) + and 200 POPI (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoinositol, 50 mol%) at 310 + K. Simulated with CHARMM36 in GROMACS 2022.4 for 500 ns (58400 atoms). Deposited + as NMRlipids Databank simulation 874 and available from https://doi.org/10.5281/zenodo.10242899. sameAs: https://doi.org/10.5281/zenodo.10242899 datePublished: '2023-12-18' license: diff --git a/Simulations/4db/c54/4dbc5440f1defe65905225286b9b446aa37082ad/8f5313af34f02d15f819a0d0dc843a780af3da87/README.yaml b/Simulations/4db/c54/4dbc5440f1defe65905225286b9b446aa37082ad/8f5313af34f02d15f819a0d0dc843a780af3da87/README.yaml index a0e5ae58cb..af42ed7ae2 100644 --- a/Simulations/4db/c54/4dbc5440f1defe65905225286b9b446aa37082ad/8f5313af34f02d15f819a0d0dc843a780af3da87/README.yaml +++ b/Simulations/4db/c54/4dbc5440f1defe65905225286b9b446aa37082ad/8f5313af34f02d15f819a0d0dc843a780af3da87/README.yaml @@ -43,9 +43,14 @@ SOFTWARE: gromacs DIR_WRK: /usr/home/bort/Databank ID: 158 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 310 K (CHARMM36 (center of mass removed independently for upper leaflet, lower leaflet and water+ions), GROMACS 5.0.4, 500 ns) [NMRlipids simulation 158] + name: Molecular dynamics trajectory of a POPC bilayer at 310 K (CHARMM36 (center + of mass removed independently for upper leaflet, lower leaflet and water+ions), + GROMACS 5.0.4, 500 ns) [NMRlipids simulation 158] alternateName: 72POPC_2239SOL_310K_rmcomm_leaflets - description: Molecular dynamics trajectory of a lipid bilayer of 72 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 310 K. Simulated with CHARMM36 (center of mass removed independently for upper leaflet, lower leaflet and water+ions) in GROMACS 5.0.4 for 500 ns (16365 atoms). Deposited as NMRlipids Databank simulation 158 and available from https://doi.org/10.5281/zenodo.1009607. + description: Molecular dynamics trajectory of a lipid bilayer of 72 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 310 K. Simulated with CHARMM36 (center of mass removed independently for upper + leaflet, lower leaflet and water+ions) in GROMACS 5.0.4 for 500 ns (16365 atoms). + Deposited as NMRlipids Databank simulation 158 and available from https://doi.org/10.5281/zenodo.1009607. sameAs: https://doi.org/10.5281/zenodo.1009607 datePublished: '2017-10-12' license: @@ -98,7 +103,8 @@ bioschema_properties: inDefinedTermSet: http://edamontology.org url: http://edamontology.org/operation_2476 - Molecular dynamics simulation (gromacs 5.0.4) - - CHARMM36 (center of mass removed independently for upper leaflet, lower leaflet and water+ions) force field + - CHARMM36 (center of mass removed independently for upper leaflet, lower leaflet + and water+ions) force field variableMeasured: - '@type': PropertyValue name: area per lipid @@ -138,7 +144,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1009607 identifier: 10.5281/zenodo.1009607 url: https://doi.org/10.5281/zenodo.1009607 - name: Set Simulations Small Pure Bilayers (72 Lipids) Using Charmm36 Ff In Gromacs (Dppc, Popc) + name: Set Simulations Small Pure Bilayers (72 Lipids) Using Charmm36 Ff In Gromacs + (Dppc, Popc) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/4e4/d45/4e4d45f15fc334edfa725ef670c7ec1f86589d3e/247e995fe4c17b8643ee8c9fb6760a383f65f024/README.yaml b/Simulations/4e4/d45/4e4d45f15fc334edfa725ef670c7ec1f86589d3e/247e995fe4c17b8643ee8c9fb6760a383f65f024/README.yaml index 20b8035029..3b0ec34303 100644 --- a/Simulations/4e4/d45/4e4d45f15fc334edfa725ef670c7ec1f86589d3e/247e995fe4c17b8643ee8c9fb6760a383f65f024/README.yaml +++ b/Simulations/4e4/d45/4e4d45f15fc334edfa725ef670c7ec1f86589d3e/247e995fe4c17b8643ee8c9fb6760a383f65f024/README.yaml @@ -46,9 +46,12 @@ EXPERIMENT: - 10.1016/j.bbamem.2011.07.022/11 ID: 405 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 313 K (ECC-lipids, GROMACS 5.1.4, 100 ns) [NMRlipids simulation 405] + name: Molecular dynamics trajectory of a POPC bilayer at 313 K (ECC-lipids, GROMACS + 5.1.4, 100 ns) [NMRlipids simulation 405] alternateName: 128POPC_6400SOL_313K - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 100 ns (36352 atoms). Deposited as NMRlipids Databank simulation 405 and available from https://doi.org/10.5281/zenodo.3335503. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 100 ns (36352 atoms). + Deposited as NMRlipids Databank simulation 405 and available from https://doi.org/10.5281/zenodo.3335503. sameAs: https://doi.org/10.5281/zenodo.3335503 datePublished: '2017-12-19' license: @@ -140,7 +143,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3335503 identifier: 10.5281/zenodo.3335503 url: https://doi.org/10.5281/zenodo.3335503 - name: Simulations of POPC lipid bilayer in water solution at various NaCl, KCl and CaCl2 concentrations using ECC-POPC force field + name: Simulations of POPC lipid bilayer in water solution at various NaCl, KCl + and CaCl2 concentrations using ECC-POPC force field publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/4ee/bee/4eebeea7a1dcb5ba4e00077ff51d30ff85230853/46b00269ba4fccb33403c48c7290d45ebd99dd33/README.yaml b/Simulations/4ee/bee/4eebeea7a1dcb5ba4e00077ff51d30ff85230853/46b00269ba4fccb33403c48c7290d45ebd99dd33/README.yaml index 0f7bd6fedb..1761b24c27 100644 --- a/Simulations/4ee/bee/4eebeea7a1dcb5ba4e00077ff51d30ff85230853/46b00269ba4fccb33403c48c7290d45ebd99dd33/README.yaml +++ b/Simulations/4ee/bee/4eebeea7a1dcb5ba4e00077ff51d30ff85230853/46b00269ba4fccb33403c48c7290d45ebd99dd33/README.yaml @@ -50,9 +50,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 857 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (68:22:11) bilayer at 300 K (CHARMM36, GROMACS 2019.5, 100 ns) [NMRlipids simulation 857] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (68:22:11) bilayer at 300 + K (CHARMM36, GROMACS 2019.5, 100 ns) [NMRlipids simulation 857] alternateName: POPC, 44 w/l, 300 K, 0.2 M CaCl2 - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 68 mol%), 64 CLA (22 mol%) and 32 CAL (11 mol%) at 300 K. Simulated with CHARMM36 in GROMACS 2019.5 for 100 ns (53536 atoms). Deposited as NMRlipids Databank simulation 857 and available from https://doi.org/10.5281/zenodo.6337813. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 68 mol%), 64 CLA (22 mol%) and 32 CAL (11 mol%) at 300 K. Simulated with CHARMM36 + in GROMACS 2019.5 for 100 ns (53536 atoms). Deposited as NMRlipids Databank simulation + 857 and available from https://doi.org/10.5281/zenodo.6337813. sameAs: https://doi.org/10.5281/zenodo.6337813 datePublished: '2022-03-08' license: diff --git a/Simulations/4f2/f97/4f2f97602e1387ad95b967b2d6fb04b353817f17/4f2f97602e1387ad95b967b2d6fb04b353817f17/README.yaml b/Simulations/4f2/f97/4f2f97602e1387ad95b967b2d6fb04b353817f17/4f2f97602e1387ad95b967b2d6fb04b353817f17/README.yaml index 6d2aa91231..e5968a5a7b 100644 --- a/Simulations/4f2/f97/4f2f97602e1387ad95b967b2d6fb04b353817f17/4f2f97602e1387ad95b967b2d6fb04b353817f17/README.yaml +++ b/Simulations/4f2/f97/4f2f97602e1387ad95b967b2d6fb04b353817f17/4f2f97602e1387ad95b967b2d6fb04b353817f17/README.yaml @@ -39,9 +39,12 @@ EXPERIMENT: FORMFACTOR: - 10.1016/j.chemphyslip.2020.104892/2 bioschema_properties: - name: Molecular dynamics trajectory of a SDPC bilayer at 303.15 K (CHARMM36m, NAMD 3, 500 ns) [NMRlipids simulation 901] + name: Molecular dynamics trajectory of a SDPC bilayer at 303.15 K (CHARMM36m, NAMD + 3, 500 ns) [NMRlipids simulation 901] alternateName: SDPC - description: Molecular dynamics trajectory of a lipid bilayer of 200 SDPC (1-stearoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine) at 303.15 K. Simulated with CHARMM36m in NAMD 3 for 500 ns (56000 atoms). Deposited as NMRlipids Databank simulation 901 and available from https://doi.org/10.5281/zenodo.18384813. + description: Molecular dynamics trajectory of a lipid bilayer of 200 SDPC (1-stearoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine) + at 303.15 K. Simulated with CHARMM36m in NAMD 3 for 500 ns (56000 atoms). Deposited + as NMRlipids Databank simulation 901 and available from https://doi.org/10.5281/zenodo.18384813. sameAs: https://doi.org/10.5281/zenodo.18384813 datePublished: '2026-01-27' license: @@ -133,7 +136,9 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.18384813 identifier: 10.5281/zenodo.18384813 url: https://doi.org/10.5281/zenodo.18384813 - name: Polyunsaturated 1-stearoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine (18:0/22:6) | SDPC lipid bilayer, 303K, CHARMM36m-WYF forcefield, NAMD 3.0.2, 2* 500 ns + name: Polyunsaturated 1-stearoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine + (18:0/22:6) | SDPC lipid bilayer, 303K, CHARMM36m-WYF forcefield, NAMD 3.0.2, + 2* 500 ns publisher: Zenodo _source: api: datacite diff --git a/Simulations/4f5/3a3/4f53a3e004f69af7030f372370c297664cce57c7/0f2ebb5148b446bdc11b954537c11d95ab1c9788/README.yaml b/Simulations/4f5/3a3/4f53a3e004f69af7030f372370c297664cce57c7/0f2ebb5148b446bdc11b954537c11d95ab1c9788/README.yaml index 81ce849a84..8e8bb64e38 100644 --- a/Simulations/4f5/3a3/4f53a3e004f69af7030f372370c297664cce57c7/0f2ebb5148b446bdc11b954537c11d95ab1c9788/README.yaml +++ b/Simulations/4f5/3a3/4f53a3e004f69af7030f372370c297664cce57c7/0f2ebb5148b446bdc11b954537c11d95ab1c9788/README.yaml @@ -49,9 +49,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 693 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (71:29) bilayer at 298.15 K (Slipids, GROMACS 2021, 1001 ns) [NMRlipids simulation 693] + name: Molecular dynamics trajectory of a POPC/CHOL (71:29) bilayer at 298.15 K (Slipids, + GROMACS 2021, 1001 ns) [NMRlipids simulation 693] alternateName: Slipids_POPC_CHOL29_S - description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 71 mol%) and 26 CHOL (cholesterol, 29 mol%) at 298.15 K. Simulated with Slipids in GROMACS 2021 for 1001 ns (24000 atoms). Deposited as NMRlipids Databank simulation 693 and available from https://doi.org/10.5281/zenodo.7022749. + description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 71 mol%) and 26 CHOL (cholesterol, 29 mol%) at 298.15 K. Simulated with Slipids + in GROMACS 2021 for 1001 ns (24000 atoms). Deposited as NMRlipids Databank simulation + 693 and available from https://doi.org/10.5281/zenodo.7022749. sameAs: https://doi.org/10.5281/zenodo.7022749 datePublished: '2022-08-23' license: diff --git a/Simulations/4f5/748/4f5748815c1beb235b960aee5cac8c6051329dc5/7515ec356a0668d62126161c159cca3e7876bb83/README.yaml b/Simulations/4f5/748/4f5748815c1beb235b960aee5cac8c6051329dc5/7515ec356a0668d62126161c159cca3e7876bb83/README.yaml index 2bcc00a7f5..4302d594b7 100644 --- a/Simulations/4f5/748/4f5748815c1beb235b960aee5cac8c6051329dc5/7515ec356a0668d62126161c159cca3e7876bb83/README.yaml +++ b/Simulations/4f5/748/4f5748815c1beb235b960aee5cac8c6051329dc5/7515ec356a0668d62126161c159cca3e7876bb83/README.yaml @@ -55,9 +55,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 196 bioschema_properties: - name: Molecular dynamics trajectory of a CLA/POPC/CAL (48:28:24) bilayer at 313 K (ECC-lipids, GROMACS 5.1.4, 300 ns) [NMRlipids simulation 196] + name: Molecular dynamics trajectory of a CLA/POPC/CAL (48:28:24) bilayer at 313 + K (ECC-lipids, GROMACS 5.1.4, 300 ns) [NMRlipids simulation 196] alternateName: 128POPC_6232SOL_110CAL_220CLA_313K_OPC4model - description: Molecular dynamics trajectory of a lipid bilayer of 220 CLA (48 mol%), 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 28 mol%) and 110 CAL (24 mol%) at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 300 ns (42410 atoms). Deposited as NMRlipids Databank simulation 196 and available from https://doi.org/10.5281/zenodo.1118980. + description: Molecular dynamics trajectory of a lipid bilayer of 220 CLA (48 mol%), + 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 28 mol%) and 110 CAL + (24 mol%) at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 300 ns (42410 + atoms). Deposited as NMRlipids Databank simulation 196 and available from https://doi.org/10.5281/zenodo.1118980. sameAs: https://doi.org/10.5281/zenodo.1118980 datePublished: '2017-12-19' license: @@ -147,7 +151,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1118980 identifier: 10.5281/zenodo.1118980 url: https://doi.org/10.5281/zenodo.1118980 - name: Simulations Of Popc Lipid Bilayer In Water Solution At Various Nacl And Cacl2 Concentrations Using Ecc-Popc Force Field And Various Water Models + name: Simulations Of Popc Lipid Bilayer In Water Solution At Various Nacl And + Cacl2 Concentrations Using Ecc-Popc Force Field And Various Water Models publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/4f5/fb4/4f5fb4c911390b50b56d06364c85910c10191c57/ea16a8b51b9d71838d911eb3cebbc69ad05600d8/README.yaml b/Simulations/4f5/fb4/4f5fb4c911390b50b56d06364c85910c10191c57/ea16a8b51b9d71838d911eb3cebbc69ad05600d8/README.yaml index 2824e59d31..9989585804 100644 --- a/Simulations/4f5/fb4/4f5fb4c911390b50b56d06364c85910c10191c57/ea16a8b51b9d71838d911eb3cebbc69ad05600d8/README.yaml +++ b/Simulations/4f5/fb4/4f5fb4c911390b50b56d06364c85910c10191c57/ea16a8b51b9d71838d911eb3cebbc69ad05600d8/README.yaml @@ -39,9 +39,12 @@ EXPERIMENT: ID: 797 AUTHORS_CONTACT: Hoeflich, Julianne bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 300 K (OpenFF, GROMACS, 200 ns) [NMRlipids simulation 797] + name: Molecular dynamics trajectory of a POPC bilayer at 300 K (OpenFF, GROMACS, + 200 ns) [NMRlipids simulation 797] alternateName: POPCandTIP3P - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 300 K. Simulated with OpenFF in GROMACS for 200 ns (32512 atoms). Deposited as NMRlipids Databank simulation 797 and available from https://doi.org/10.5281/zenodo.10783846. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 300 K. Simulated with OpenFF in GROMACS for 200 ns (32512 atoms). Deposited + as NMRlipids Databank simulation 797 and available from https://doi.org/10.5281/zenodo.10783846. sameAs: https://doi.org/10.5281/zenodo.10783846 datePublished: '2024-03-06' license: diff --git a/Simulations/4f7/da7/4f7da716a581be4f931d2e9a2890872bec19c66a/4f7da716a581be4f931d2e9a2890872bec19c66a/README.yaml b/Simulations/4f7/da7/4f7da716a581be4f931d2e9a2890872bec19c66a/4f7da716a581be4f931d2e9a2890872bec19c66a/README.yaml index f814a0a885..50b758a2b0 100644 --- a/Simulations/4f7/da7/4f7da716a581be4f931d2e9a2890872bec19c66a/4f7da716a581be4f931d2e9a2890872bec19c66a/README.yaml +++ b/Simulations/4f7/da7/4f7da716a581be4f931d2e9a2890872bec19c66a/4f7da716a581be4f931d2e9a2890872bec19c66a/README.yaml @@ -46,9 +46,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 738 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (56:22:22) bilayer at 303 K (Charmm-Drude polarizable; system has been equilibriated using Charmm36, OPENMM 7.4.1, 521 ns) [NMRlipids simulation 738] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (56:22:22) bilayer at 303 + K (Charmm-Drude polarizable; system has been equilibriated using Charmm36, OPENMM + 7.4.1, 521 ns) [NMRlipids simulation 738] alternateName: 128POPC_6400SOL_51NaCl_303K - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 56 mol%), 51 CLA (22 mol%) and 51 SOD (22 mol%) at 303 K. Simulated with Charmm-Drude polarizable; system has been equilibriated using Charmm36 in OPENMM 7.4.1 for 521 ns (57036 atoms). Deposited as NMRlipids Databank simulation 738 and available from https://doi.org/10.5281/zenodo.7591753. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 56 mol%), 51 CLA (22 mol%) and 51 SOD (22 mol%) at 303 K. Simulated with Charmm-Drude + polarizable; system has been equilibriated using Charmm36 in OPENMM 7.4.1 for + 521 ns (57036 atoms). Deposited as NMRlipids Databank simulation 738 and available + from https://doi.org/10.5281/zenodo.7591753. sameAs: https://doi.org/10.5281/zenodo.7591753 datePublished: '2020-08-19' license: @@ -140,7 +146,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.7591753 identifier: 10.5281/zenodo.7591753 url: https://doi.org/10.5281/zenodo.7591753 - name: Pure POPC Membrane with 450mM NaCl simulations using Drude Polarizable Force Field and OpenMM + name: Pure POPC Membrane with 450mM NaCl simulations using Drude Polarizable Force + Field and OpenMM publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/4f8/75f/4f875f2005a840efeb6c24ae3ee03911f204810c/8eaaf431e4f0668ee9983c72a830d4aa911e90c3/README.yaml b/Simulations/4f8/75f/4f875f2005a840efeb6c24ae3ee03911f204810c/8eaaf431e4f0668ee9983c72a830d4aa911e90c3/README.yaml index 0ba294a4c3..1e6993eef3 100644 --- a/Simulations/4f8/75f/4f875f2005a840efeb6c24ae3ee03911f204810c/8eaaf431e4f0668ee9983c72a830d4aa911e90c3/README.yaml +++ b/Simulations/4f8/75f/4f875f2005a840efeb6c24ae3ee03911f204810c/8eaaf431e4f0668ee9983c72a830d4aa911e90c3/README.yaml @@ -51,9 +51,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 843 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (85:8:8) bilayer at 310 K (CHARMM36, GROMACS, 1000 ns) [NMRlipids simulation 843] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (85:8:8) bilayer at 310 K + (CHARMM36, GROMACS, 1000 ns) [NMRlipids simulation 843] alternateName: POPC_111mM_NaCl_CHARMM36 - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 85 mol%), 18 CLA (8 mol%) and 18 SOD (8 mol%) at 310 K. Simulated with CHARMM36 in GROMACS for 1000 ns (53836 atoms). Deposited as NMRlipids Databank simulation 843 and available from https://doi.org/10.5281/zenodo.10464958. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 85 mol%), 18 CLA (8 mol%) and 18 SOD (8 mol%) at 310 K. Simulated with CHARMM36 + in GROMACS for 1000 ns (53836 atoms). Deposited as NMRlipids Databank simulation + 843 and available from https://doi.org/10.5281/zenodo.10464958. sameAs: https://doi.org/10.5281/zenodo.10464958 datePublished: '2024-01-06' license: diff --git a/Simulations/4fb/255/4fb255b704c3d6a78c006a1b068e14c659d9667b/8e7e5deb23cdd19f7239116293ccf2a7995ecbbb/README.yaml b/Simulations/4fb/255/4fb255b704c3d6a78c006a1b068e14c659d9667b/8e7e5deb23cdd19f7239116293ccf2a7995ecbbb/README.yaml index dcd52a3ca6..00a079a24f 100644 --- a/Simulations/4fb/255/4fb255b704c3d6a78c006a1b068e14c659d9667b/8e7e5deb23cdd19f7239116293ccf2a7995ecbbb/README.yaml +++ b/Simulations/4fb/255/4fb255b704c3d6a78c006a1b068e14c659d9667b/8e7e5deb23cdd19f7239116293ccf2a7995ecbbb/README.yaml @@ -55,9 +55,14 @@ DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 229 AUTHORS_CONTACT: Javanainen, Matti bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPG/SOD/CLA/CAL (28:28:28:10:5) bilayer at 298 K (Slipids, GROMACS, 1000 ns) [NMRlipids simulation 229] + name: Molecular dynamics trajectory of a POPC/POPG/SOD/CLA/CAL (28:28:28:10:5) bilayer + at 298 K (Slipids, GROMACS, 1000 ns) [NMRlipids simulation 229] alternateName: POPCPOPG(1_1)_slipids - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 28 mol%), 128 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 28 mol%), 128 SOD (28 mol%), 46 CLA (10 mol%) and 23 CAL (5 mol%) at 298 K. Simulated with Slipids in GROMACS for 1000 ns (72005 atoms). Deposited as NMRlipids Databank simulation 229 and available from https://doi.org/10.5281/zenodo.3613573. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 28 mol%), 128 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 28 mol%), + 128 SOD (28 mol%), 46 CLA (10 mol%) and 23 CAL (5 mol%) at 298 K. Simulated with + Slipids in GROMACS for 1000 ns (72005 atoms). Deposited as NMRlipids Databank + simulation 229 and available from https://doi.org/10.5281/zenodo.3613573. sameAs: https://doi.org/10.5281/zenodo.3613573 datePublished: '2020-01-13' license: @@ -148,7 +153,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3613573 identifier: 10.5281/zenodo.3613573 url: https://doi.org/10.5281/zenodo.3613573 - name: Simulations of POPC:POPG 1:1 membranes with varying levels of CaCl_2 using the Slipids force field + name: Simulations of POPC:POPG 1:1 membranes with varying levels of CaCl_2 using + the Slipids force field publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/4fb/255/4fb255b704c3d6a78c006a1b068e14c659d9667b/e58237fa93ac53f3ddc545f4ff4148d6af982448/README.yaml b/Simulations/4fb/255/4fb255b704c3d6a78c006a1b068e14c659d9667b/e58237fa93ac53f3ddc545f4ff4148d6af982448/README.yaml index 4e34619ec4..a475cf885c 100644 --- a/Simulations/4fb/255/4fb255b704c3d6a78c006a1b068e14c659d9667b/e58237fa93ac53f3ddc545f4ff4148d6af982448/README.yaml +++ b/Simulations/4fb/255/4fb255b704c3d6a78c006a1b068e14c659d9667b/e58237fa93ac53f3ddc545f4ff4148d6af982448/README.yaml @@ -55,9 +55,14 @@ DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 230 AUTHORS_CONTACT: Javanainen, Matti bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPG/SOD/CLA/CAL (28:28:28:10:5) bilayer at 298 K (Slipids, GROMACS, 479 ns) [NMRlipids simulation 230] + name: Molecular dynamics trajectory of a POPC/POPG/SOD/CLA/CAL (28:28:28:10:5) bilayer + at 298 K (Slipids, GROMACS, 479 ns) [NMRlipids simulation 230] alternateName: POPCPOPG(1_1)_slipids - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 28 mol%), 128 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 28 mol%), 128 SOD (28 mol%), 46 CLA (10 mol%) and 23 CAL (5 mol%) at 298 K. Simulated with Slipids in GROMACS for 479 ns (72005 atoms). Deposited as NMRlipids Databank simulation 230 and available from https://doi.org/10.5281/zenodo.3613573. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 28 mol%), 128 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 28 mol%), + 128 SOD (28 mol%), 46 CLA (10 mol%) and 23 CAL (5 mol%) at 298 K. Simulated with + Slipids in GROMACS for 479 ns (72005 atoms). Deposited as NMRlipids Databank simulation + 230 and available from https://doi.org/10.5281/zenodo.3613573. sameAs: https://doi.org/10.5281/zenodo.3613573 datePublished: '2020-01-13' license: @@ -148,7 +153,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3613573 identifier: 10.5281/zenodo.3613573 url: https://doi.org/10.5281/zenodo.3613573 - name: Simulations of POPC:POPG 1:1 membranes with varying levels of CaCl_2 using the Slipids force field + name: Simulations of POPC:POPG 1:1 membranes with varying levels of CaCl_2 using + the Slipids force field publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/500/560/5005607fb8221bb24a4b7d263207246bed95cded/ba583ae780ed82e7b8145ce3855ef9775a2cd350/README.yaml b/Simulations/500/560/5005607fb8221bb24a4b7d263207246bed95cded/ba583ae780ed82e7b8145ce3855ef9775a2cd350/README.yaml index 278d4cb2f8..22d5ae3247 100644 --- a/Simulations/500/560/5005607fb8221bb24a4b7d263207246bed95cded/ba583ae780ed82e7b8145ce3855ef9775a2cd350/README.yaml +++ b/Simulations/500/560/5005607fb8221bb24a4b7d263207246bed95cded/ba583ae780ed82e7b8145ce3855ef9775a2cd350/README.yaml @@ -44,9 +44,13 @@ EXPERIMENT: POPS: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a POPS/POT (50:50) bilayer at 298 K (Macrog, GROMACS 2016.3, 200 ns) [NMRlipids simulation 881] + name: Molecular dynamics trajectory of a POPS/POT (50:50) bilayer at 298 K (Macrog, + GROMACS 2016.3, 200 ns) [NMRlipids simulation 881] alternateName: Bilayer - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 50 mol%) and 128 POT (50 mol%) at 298 K. Simulated with Macrog in GROMACS 2016.3 for 200 ns (29824 atoms). Deposited as NMRlipids Databank simulation 881 and available from https://doi.org/10.5281/zenodo.1434990. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, + 50 mol%) and 128 POT (50 mol%) at 298 K. Simulated with Macrog in GROMACS 2016.3 + for 200 ns (29824 atoms). Deposited as NMRlipids Databank simulation 881 and available + from https://doi.org/10.5281/zenodo.1434990. sameAs: https://doi.org/10.5281/zenodo.1434990 datePublished: '2018-09-25' license: diff --git a/Simulations/502/d93/502d93642bcfca282d7f28732b8d67384ea26d9d/7d08980a2dea2e16bd9d44be7484e6d49d6c8bd0/README.yaml b/Simulations/502/d93/502d93642bcfca282d7f28732b8d67384ea26d9d/7d08980a2dea2e16bd9d44be7484e6d49d6c8bd0/README.yaml index 6c1474c598..1fff620dc0 100644 --- a/Simulations/502/d93/502d93642bcfca282d7f28732b8d67384ea26d9d/7d08980a2dea2e16bd9d44be7484e6d49d6c8bd0/README.yaml +++ b/Simulations/502/d93/502d93642bcfca282d7f28732b8d67384ea26d9d/7d08980a2dea2e16bd9d44be7484e6d49d6c8bd0/README.yaml @@ -51,9 +51,13 @@ EXPERIMENT: CHOL: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a DOPC/CHOL (71:29) bilayer at 333.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 648] + name: Molecular dynamics trajectory of a DOPC/CHOL (71:29) bilayer at 333.15 K (CHARMM36, + GROMACS, 1001 ns) [NMRlipids simulation 648] alternateName: 64DOPC_26CHOL_4500SOL_333K - description: Molecular dynamics trajectory of a lipid bilayer of 64 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, 71 mol%) and 26 CHOL (cholesterol, 29 mol%) at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (24256 atoms). Deposited as NMRlipids Databank simulation 648 and available from https://doi.org/10.5281/zenodo.6943929. + description: Molecular dynamics trajectory of a lipid bilayer of 64 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, + 71 mol%) and 26 CHOL (cholesterol, 29 mol%) at 333.15 K. Simulated with CHARMM36 + in GROMACS for 1001 ns (24256 atoms). Deposited as NMRlipids Databank simulation + 648 and available from https://doi.org/10.5281/zenodo.6943929. sameAs: https://doi.org/10.5281/zenodo.6943929 datePublished: '2022-07-30' license: diff --git a/Simulations/503/bbb/503bbb64862a9cf4f574189806dfdd25f88e6a14/41807262ab583f3f5dd05af4b7786bc6889239fc/README.yaml b/Simulations/503/bbb/503bbb64862a9cf4f574189806dfdd25f88e6a14/41807262ab583f3f5dd05af4b7786bc6889239fc/README.yaml index ce0d4d1b60..e43bef9616 100644 --- a/Simulations/503/bbb/503bbb64862a9cf4f574189806dfdd25f88e6a14/41807262ab583f3f5dd05af4b7786bc6889239fc/README.yaml +++ b/Simulations/503/bbb/503bbb64862a9cf4f574189806dfdd25f88e6a14/41807262ab583f3f5dd05af4b7786bc6889239fc/README.yaml @@ -48,9 +48,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 141 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (59:41) bilayer at 310 K (MacRog, GROMACS 4.6, 500 ns) [NMRlipids simulation 141] + name: Molecular dynamics trajectory of a POPC/CHOL (59:41) bilayer at 310 K (MacRog, + GROMACS 4.6, 500 ns) [NMRlipids simulation 141] alternateName: 76POPC_52CHOL_6400SOL_310K - description: Molecular dynamics trajectory of a lipid bilayer of 76 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 59 mol%) and 52 CHOL (cholesterol, 41 mol%) at 310 K. Simulated with MacRog in GROMACS 4.6 for 500 ns (33232 atoms). Deposited as NMRlipids Databank simulation 141 and available from https://doi.org/10.5281/zenodo.3252052. + description: Molecular dynamics trajectory of a lipid bilayer of 76 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 59 mol%) and 52 CHOL (cholesterol, 41 mol%) at 310 K. Simulated with MacRog in + GROMACS 4.6 for 500 ns (33232 atoms). Deposited as NMRlipids Databank simulation + 141 and available from https://doi.org/10.5281/zenodo.3252052. sameAs: https://doi.org/10.5281/zenodo.3252052 datePublished: '2015-01-11' license: @@ -143,7 +147,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3252052 identifier: 10.5281/zenodo.3252052 url: https://doi.org/10.5281/zenodo.3252052 - name: POPC/Cholesterol @ 310K. 0, 10, 40, 50 and 60 mol-% cholesterol. Model by Maciejewski and Rog + name: POPC/Cholesterol @ 310K. 0, 10, 40, 50 and 60 mol-% cholesterol. Model by + Maciejewski and Rog publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/508/748/5087483af99bfbd427630e5974e20aea6d34b2ae/4062f0e472c77353fc638996ae7dfcb505f3433e/README.yaml b/Simulations/508/748/5087483af99bfbd427630e5974e20aea6d34b2ae/4062f0e472c77353fc638996ae7dfcb505f3433e/README.yaml index b4546de75b..c65131bee8 100644 --- a/Simulations/508/748/5087483af99bfbd427630e5974e20aea6d34b2ae/4062f0e472c77353fc638996ae7dfcb505f3433e/README.yaml +++ b/Simulations/508/748/5087483af99bfbd427630e5974e20aea6d34b2ae/4062f0e472c77353fc638996ae7dfcb505f3433e/README.yaml @@ -54,9 +54,14 @@ TRJ: - - traj.xtc ID: 253 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPG/SOD/CLA/CAL (25:25:25:18:9) bilayer at 298 K (lipid17ecc, GROMACS, 300 ns) [NMRlipids simulation 253] + name: Molecular dynamics trajectory of a POPC/POPG/SOD/CLA/CAL (25:25:25:18:9) bilayer + at 298 K (lipid17ecc, GROMACS, 300 ns) [NMRlipids simulation 253] alternateName: POPC:POPG(1:1)_T298K_100mM_CaCl - description: Molecular dynamics trajectory of a lipid bilayer of 150 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 25 mol%), 150 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 25 mol%), 150 SOD (25 mol%), 108 CLA (18 mol%) and 54 CAL (9 mol%) at 298 K. Simulated with lipid17ecc in GROMACS for 300 ns (129057 atoms). Deposited as NMRlipids Databank simulation 253 and available from https://doi.org/10.5281/zenodo.3855729. + description: Molecular dynamics trajectory of a lipid bilayer of 150 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 25 mol%), 150 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 25 mol%), + 150 SOD (25 mol%), 108 CLA (18 mol%) and 54 CAL (9 mol%) at 298 K. Simulated with + lipid17ecc in GROMACS for 300 ns (129057 atoms). Deposited as NMRlipids Databank + simulation 253 and available from https://doi.org/10.5281/zenodo.3855729. sameAs: https://doi.org/10.5281/zenodo.3855729 datePublished: '2020-05-26' license: @@ -147,7 +152,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3855729 identifier: 10.5281/zenodo.3855729 url: https://doi.org/10.5281/zenodo.3855729 - name: ECC-LIPID17 POPC-POPG 50:50 MD simulation, Na+ counterions and 100mM CaCl2, 298K + name: ECC-LIPID17 POPC-POPG 50:50 MD simulation, Na+ counterions and 100mM CaCl2, + 298K publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/509/c36/509c361e11083ae342e56bf9ab505fff8baca832/dddadda65a74e26313a75581d2e2c5326ca4f428/README.yaml b/Simulations/509/c36/509c361e11083ae342e56bf9ab505fff8baca832/dddadda65a74e26313a75581d2e2c5326ca4f428/README.yaml index 536790ffd3..0a6994b155 100644 --- a/Simulations/509/c36/509c361e11083ae342e56bf9ab505fff8baca832/dddadda65a74e26313a75581d2e2c5326ca4f428/README.yaml +++ b/Simulations/509/c36/509c361e11083ae342e56bf9ab505fff8baca832/dddadda65a74e26313a75581d2e2c5326ca4f428/README.yaml @@ -48,9 +48,12 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/1 ID: 830 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 298 K (C36_Slipids_Hybrid, GROMACS 2024.3, 500 ns) [NMRlipids simulation 830] + name: Molecular dynamics trajectory of a POPC bilayer at 298 K (C36_Slipids_Hybrid, + GROMACS 2024.3, 500 ns) [NMRlipids simulation 830] alternateName: POPC_hybrid_c36mdp - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 298 K. Simulated with C36_Slipids_Hybrid in GROMACS 2024.3 for 500 ns (36352 atoms). Deposited as NMRlipids Databank simulation 830 and available from https://doi.org/10.5281/zenodo.15172176. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 298 K. Simulated with C36_Slipids_Hybrid in GROMACS 2024.3 for 500 ns (36352 + atoms). Deposited as NMRlipids Databank simulation 830 and available from https://doi.org/10.5281/zenodo.15172176. sameAs: https://doi.org/10.5281/zenodo.15172176 datePublished: '2025-04-08' license: diff --git a/Simulations/50a/869/50a869e592b5cb04f2139c462da1fd7814832acd/4416de72d1d15b560aef6adf7222ea774c90b53f/README.yaml b/Simulations/50a/869/50a869e592b5cb04f2139c462da1fd7814832acd/4416de72d1d15b560aef6adf7222ea774c90b53f/README.yaml index 187603f1dd..8a52fc98bb 100644 --- a/Simulations/50a/869/50a869e592b5cb04f2139c462da1fd7814832acd/4416de72d1d15b560aef6adf7222ea774c90b53f/README.yaml +++ b/Simulations/50a/869/50a869e592b5cb04f2139c462da1fd7814832acd/4416de72d1d15b560aef6adf7222ea774c90b53f/README.yaml @@ -52,9 +52,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 503 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPG/SOD (33:33:33) bilayer at 298 K (Lipid17, GROMACS, 200 ns) [NMRlipids simulation 503] + name: Molecular dynamics trajectory of a POPC/POPG/SOD (33:33:33) bilayer at 298 + K (Lipid17, GROMACS, 200 ns) [NMRlipids simulation 503] alternateName: 150POPC_150POPG_31572SOL_150SOD_298K - description: Molecular dynamics trajectory of a lipid bilayer of 150 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 33 mol%), 150 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 33 mol%) and 150 SOD (33 mol%) at 298 K. Simulated with Lipid17 in GROMACS for 200 ns (134016 atoms). Deposited as NMRlipids Databank simulation 503 and available from https://doi.org/10.5281/zenodo.3857816. + description: Molecular dynamics trajectory of a lipid bilayer of 150 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 33 mol%), 150 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 33 mol%) + and 150 SOD (33 mol%) at 298 K. Simulated with Lipid17 in GROMACS for 200 ns (134016 + atoms). Deposited as NMRlipids Databank simulation 503 and available from https://doi.org/10.5281/zenodo.3857816. sameAs: https://doi.org/10.5281/zenodo.3857816 datePublished: '2019-10-28' license: diff --git a/Simulations/510/12c/51012c474bca21c273cf9f98a616e17fdd5d6a70/a782edd245a4182888ec0357eac37570fd7f1a4a/README.yaml b/Simulations/510/12c/51012c474bca21c273cf9f98a616e17fdd5d6a70/a782edd245a4182888ec0357eac37570fd7f1a4a/README.yaml index 192a760986..2699e62cbc 100644 --- a/Simulations/510/12c/51012c474bca21c273cf9f98a616e17fdd5d6a70/a782edd245a4182888ec0357eac37570fd7f1a4a/README.yaml +++ b/Simulations/510/12c/51012c474bca21c273cf9f98a616e17fdd5d6a70/a782edd245a4182888ec0357eac37570fd7f1a4a/README.yaml @@ -51,9 +51,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/8 ID: 694 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (62:38) bilayer at 298.15 K (Lipid17, GROMACS 2021, 1001 ns) [NMRlipids simulation 694] + name: Molecular dynamics trajectory of a POPC/CHOL (62:38) bilayer at 298.15 K (Lipid17, + GROMACS 2021, 1001 ns) [NMRlipids simulation 694] alternateName: Lipid17_POPC_CHOL38_M - description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 62 mol%) and 160 CHOL (cholesterol, 38 mol%) at 298.15 K. Simulated with Lipid17 in GROMACS 2021 for 1001 ns (108544 atoms). Deposited as NMRlipids Databank simulation 694 and available from https://doi.org/10.5281/zenodo.6992065. + description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 62 mol%) and 160 CHOL (cholesterol, 38 mol%) at 298.15 K. Simulated with Lipid17 + in GROMACS 2021 for 1001 ns (108544 atoms). Deposited as NMRlipids Databank simulation + 694 and available from https://doi.org/10.5281/zenodo.6992065. sameAs: https://doi.org/10.5281/zenodo.6992065 datePublished: '2022-08-15' license: diff --git a/Simulations/511/e6d/511e6d37157865a0e3c3b28683369c97f133449c/8a6df459f0310263b3bab211c0f4257e7bd3698b/README.yaml b/Simulations/511/e6d/511e6d37157865a0e3c3b28683369c97f133449c/8a6df459f0310263b3bab211c0f4257e7bd3698b/README.yaml index d460c892a1..ce8698356c 100644 --- a/Simulations/511/e6d/511e6d37157865a0e3c3b28683369c97f133449c/8a6df459f0310263b3bab211c0f4257e7bd3698b/README.yaml +++ b/Simulations/511/e6d/511e6d37157865a0e3c3b28683369c97f133449c/8a6df459f0310263b3bab211c0f4257e7bd3698b/README.yaml @@ -53,9 +53,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 69 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (84:8:8) bilayer at 310 K (GROMOS-CKP, GROMACS 5.1.2, 100 ns) [NMRlipids simulation 69] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (84:8:8) bilayer at 310 K + (GROMOS-CKP, GROMACS 5.1.2, 100 ns) [NMRlipids simulation 69] alternateName: 500POPC_25000SOL_48SOD_48CLA_310K_GROMOS-CKP - description: Molecular dynamics trajectory of a lipid bilayer of 500 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 84 mol%), 48 CLA (8 mol%) and 48 SOD (8 mol%) at 310 K. Simulated with GROMOS-CKP in GROMACS 5.1.2 for 100 ns (101096 atoms). Deposited as NMRlipids Databank simulation 69 and available from https://doi.org/10.5281/zenodo.2574691. + description: Molecular dynamics trajectory of a lipid bilayer of 500 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 84 mol%), 48 CLA (8 mol%) and 48 SOD (8 mol%) at 310 K. Simulated with GROMOS-CKP + in GROMACS 5.1.2 for 100 ns (101096 atoms). Deposited as NMRlipids Databank simulation + 69 and available from https://doi.org/10.5281/zenodo.2574691. sameAs: https://doi.org/10.5281/zenodo.2574691 datePublished: '2019-02-22' license: diff --git a/Simulations/521/c91/521c91eb270f44c9cde1da65eeae93b11f0dd325/f11b2586ed6ccfb02264890be54196542ef5d1f8/README.yaml b/Simulations/521/c91/521c91eb270f44c9cde1da65eeae93b11f0dd325/f11b2586ed6ccfb02264890be54196542ef5d1f8/README.yaml index bfef21eb18..63d3c11a0b 100644 --- a/Simulations/521/c91/521c91eb270f44c9cde1da65eeae93b11f0dd325/f11b2586ed6ccfb02264890be54196542ef5d1f8/README.yaml +++ b/Simulations/521/c91/521c91eb270f44c9cde1da65eeae93b11f0dd325/f11b2586ed6ccfb02264890be54196542ef5d1f8/README.yaml @@ -50,9 +50,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 21 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (82:9:9) bilayer at 310 K (CHARMM36, GROMACS 5.0.6, 500 ns) [NMRlipids simulation 21] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (82:9:9) bilayer at 310 K + (CHARMM36, GROMACS 5.0.6, 500 ns) [NMRlipids simulation 21] alternateName: 512POPC_20480SOL_55SOD_55CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 512 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 82 mol%), 55 CLA (9 mol%) and 55 SOD (9 mol%) at 310 K. Simulated with CHARMM36 in GROMACS 5.0.6 for 500 ns (130158 atoms). Deposited as NMRlipids Databank simulation 21 and available from https://doi.org/10.5281/zenodo.1010083. + description: Molecular dynamics trajectory of a lipid bilayer of 512 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 82 mol%), 55 CLA (9 mol%) and 55 SOD (9 mol%) at 310 K. Simulated with CHARMM36 + in GROMACS 5.0.6 for 500 ns (130158 atoms). Deposited as NMRlipids Databank simulation + 21 and available from https://doi.org/10.5281/zenodo.1010083. sameAs: https://doi.org/10.5281/zenodo.1010083 datePublished: '2017-10-12' license: diff --git a/Simulations/523/4c1/5234c14bc577e2e76fb6f986c03e28f1ae7a8beb/668d1aedd492133c9a16aa32c20961aca97b1606/README.yaml b/Simulations/523/4c1/5234c14bc577e2e76fb6f986c03e28f1ae7a8beb/668d1aedd492133c9a16aa32c20961aca97b1606/README.yaml index 1405a1c43d..1ad74ae510 100644 --- a/Simulations/523/4c1/5234c14bc577e2e76fb6f986c03e28f1ae7a8beb/668d1aedd492133c9a16aa32c20961aca97b1606/README.yaml +++ b/Simulations/523/4c1/5234c14bc577e2e76fb6f986c03e28f1ae7a8beb/668d1aedd492133c9a16aa32c20961aca97b1606/README.yaml @@ -48,9 +48,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 148 bioschema_properties: - name: Molecular dynamics trajectory of a CHOL/POPC (50:50) bilayer at 310 K (MacRog, GROMACS 4.6, 500 ns) [NMRlipids simulation 148] + name: Molecular dynamics trajectory of a CHOL/POPC (50:50) bilayer at 310 K (MacRog, + GROMACS 4.6, 500 ns) [NMRlipids simulation 148] alternateName: 64POPC_64CHOL_6400SOL_310K - description: Molecular dynamics trajectory of a lipid bilayer of 64 CHOL (cholesterol, 50 mol%) and 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 50 mol%) at 310 K. Simulated with MacRog in GROMACS 4.6 for 500 ns (32512 atoms). Deposited as NMRlipids Databank simulation 148 and available from https://doi.org/10.5281/zenodo.3252052. + description: Molecular dynamics trajectory of a lipid bilayer of 64 CHOL (cholesterol, + 50 mol%) and 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 50 mol%) + at 310 K. Simulated with MacRog in GROMACS 4.6 for 500 ns (32512 atoms). Deposited + as NMRlipids Databank simulation 148 and available from https://doi.org/10.5281/zenodo.3252052. sameAs: https://doi.org/10.5281/zenodo.3252052 datePublished: '2015-01-11' license: @@ -143,7 +147,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3252052 identifier: 10.5281/zenodo.3252052 url: https://doi.org/10.5281/zenodo.3252052 - name: POPC/Cholesterol @ 310K. 0, 10, 40, 50 and 60 mol-% cholesterol. Model by Maciejewski and Rog + name: POPC/Cholesterol @ 310K. 0, 10, 40, 50 and 60 mol-% cholesterol. Model by + Maciejewski and Rog publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/52e/142/52e1425c86de88b82dc50fc6539269b4e73b3a61/cac0f8f72a05076af7c53c7a17bf05f20666c5d7/README.yaml b/Simulations/52e/142/52e1425c86de88b82dc50fc6539269b4e73b3a61/cac0f8f72a05076af7c53c7a17bf05f20666c5d7/README.yaml index 800c1dd6b7..abcf0e64c9 100644 --- a/Simulations/52e/142/52e1425c86de88b82dc50fc6539269b4e73b3a61/cac0f8f72a05076af7c53c7a17bf05f20666c5d7/README.yaml +++ b/Simulations/52e/142/52e1425c86de88b82dc50fc6539269b4e73b3a61/cac0f8f72a05076af7c53c7a17bf05f20666c5d7/README.yaml @@ -59,9 +59,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 102 bioschema_properties: - name: Molecular dynamics trajectory of a DMPC/CLA/DMTAP (88:6:6) bilayer at 323 K (Berger with DMTAP modification by Gurtovenko et al., GROMACS 3.x, 110 ns) [NMRlipids simulation 102] + name: Molecular dynamics trajectory of a DMPC/CLA/DMTAP (88:6:6) bilayer at 323 + K (Berger with DMTAP modification by Gurtovenko et al., GROMACS 3.x, 110 ns) [NMRlipids + simulation 102] alternateName: 120DMPC_8DMTAP_8CLA_5099SOL_323K_Berger - description: Molecular dynamics trajectory of a lipid bilayer of 120 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine, 88 mol%), 8 CLA (6 mol%) and 8 DMTAP (1,2-dimyristoyl-3-trimethylammonium-propane, 6 mol%) at 323 K. Simulated with Berger with DMTAP modification by Gurtovenko et al. in GROMACS 3.x for 110 ns (21137 atoms). Deposited as NMRlipids Databank simulation 102 and available from https://doi.org/10.5281/zenodo.51639. + description: Molecular dynamics trajectory of a lipid bilayer of 120 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine, + 88 mol%), 8 CLA (6 mol%) and 8 DMTAP (1,2-dimyristoyl-3-trimethylammonium-propane, + 6 mol%) at 323 K. Simulated with Berger with DMTAP modification by Gurtovenko + et al. in GROMACS 3.x for 110 ns (21137 atoms). Deposited as NMRlipids Databank + simulation 102 and available from https://doi.org/10.5281/zenodo.51639. sameAs: https://doi.org/10.5281/zenodo.51639 datePublished: '2016-05-19' license: @@ -157,7 +163,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.51639 identifier: 10.5281/zenodo.51639 url: https://doi.org/10.5281/zenodo.51639 - name: 'Molecular dynamics simulation trajectory of a cationic lipid bilayer: 6/94 mol% DMTAP/DMPC' + name: 'Molecular dynamics simulation trajectory of a cationic lipid bilayer: 6/94 + mol% DMTAP/DMPC' publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/532/695/5326957d67eb0355d0eccf6aac9d9a44fd984777/48e776c91986eeb05d8d407567423c42bbc6126e/README.yaml b/Simulations/532/695/5326957d67eb0355d0eccf6aac9d9a44fd984777/48e776c91986eeb05d8d407567423c42bbc6126e/README.yaml index 47fd534fed..2b49977743 100644 --- a/Simulations/532/695/5326957d67eb0355d0eccf6aac9d9a44fd984777/48e776c91986eeb05d8d407567423c42bbc6126e/README.yaml +++ b/Simulations/532/695/5326957d67eb0355d0eccf6aac9d9a44fd984777/48e776c91986eeb05d8d407567423c42bbc6126e/README.yaml @@ -60,9 +60,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 14 bioschema_properties: - name: Molecular dynamics trajectory of a CLA/DMTAP/DMPC (43:43:14) bilayer at 323 K (Berger with DMTAP modification by Gurtovenko et al., GROMACS 3.x, 110 ns) [NMRlipids simulation 14] + name: Molecular dynamics trajectory of a CLA/DMTAP/DMPC (43:43:14) bilayer at 323 + K (Berger with DMTAP modification by Gurtovenko et al., GROMACS 3.x, 110 ns) [NMRlipids + simulation 14] alternateName: 32DMPC_96DMTAP_96CLA_5496SOL_323K - description: Molecular dynamics trajectory of a lipid bilayer of 96 CLA (43 mol%), 96 DMTAP (1,2-dimyristoyl-3-trimethylammonium-propane, 43 mol%) and 32 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine, 14 mol%) at 323 K. Simulated with Berger with DMTAP modification by Gurtovenko et al. in GROMACS 3.x for 110 ns (21800 atoms). Deposited as NMRlipids Databank simulation 14 and available from https://doi.org/10.5281/zenodo.51747. + description: Molecular dynamics trajectory of a lipid bilayer of 96 CLA (43 mol%), + 96 DMTAP (1,2-dimyristoyl-3-trimethylammonium-propane, 43 mol%) and 32 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine, + 14 mol%) at 323 K. Simulated with Berger with DMTAP modification by Gurtovenko + et al. in GROMACS 3.x for 110 ns (21800 atoms). Deposited as NMRlipids Databank + simulation 14 and available from https://doi.org/10.5281/zenodo.51747. sameAs: https://doi.org/10.5281/zenodo.51747 datePublished: '2016-05-20' license: @@ -159,7 +165,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.51747 identifier: 10.5281/zenodo.51747 url: https://doi.org/10.5281/zenodo.51747 - name: 'Molecular dynamics simulation trajectory of a cationic lipid bilayer: 75/25 mol% DMTAP/DMPC' + name: 'Molecular dynamics simulation trajectory of a cationic lipid bilayer: 75/25 + mol% DMTAP/DMPC' publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/533/c28/533c2888626a4d407e7c3b147f2738ccbf538d66/65ab59ecf0b2135b6bccea76d602e91b5403d853/README.yaml b/Simulations/533/c28/533c2888626a4d407e7c3b147f2738ccbf538d66/65ab59ecf0b2135b6bccea76d602e91b5403d853/README.yaml index b46e68fdf1..0a828f7032 100644 --- a/Simulations/533/c28/533c2888626a4d407e7c3b147f2738ccbf538d66/65ab59ecf0b2135b6bccea76d602e91b5403d853/README.yaml +++ b/Simulations/533/c28/533c2888626a4d407e7c3b147f2738ccbf538d66/65ab59ecf0b2135b6bccea76d602e91b5403d853/README.yaml @@ -52,9 +52,13 @@ EXPERIMENT: POPC: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/POT (81:9:9) bilayer at 298.15 K (CHARMM36m, GROMACS 2020.1, 1203 ns) [NMRlipids simulation 773] + name: Molecular dynamics trajectory of a POPC/CLA/POT (81:9:9) bilayer at 298.15 + K (CHARMM36m, GROMACS 2020.1, 1203 ns) [NMRlipids simulation 773] alternateName: POPC_298K - description: Molecular dynamics trajectory of a lipid bilayer of 300 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 81 mol%), 35 CLA (9 mol%) and 35 POT (9 mol%) at 298.15 K. Simulated with CHARMM36m in GROMACS 2020.1 for 1203 ns (80791 atoms). Deposited as NMRlipids Databank simulation 773 and available from https://doi.org/10.5281/zenodo.8370414. + description: Molecular dynamics trajectory of a lipid bilayer of 300 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 81 mol%), 35 CLA (9 mol%) and 35 POT (9 mol%) at 298.15 K. Simulated with CHARMM36m + in GROMACS 2020.1 for 1203 ns (80791 atoms). Deposited as NMRlipids Databank simulation + 773 and available from https://doi.org/10.5281/zenodo.8370414. sameAs: https://doi.org/10.5281/zenodo.8370414 datePublished: '2023-09-22' license: diff --git a/Simulations/533/cf5/533cf52de205e9e56c936c912dde6d8ee5c035cc/533cf52de205e9e56c936c912dde6d8ee5c035cc/README.yaml b/Simulations/533/cf5/533cf52de205e9e56c936c912dde6d8ee5c035cc/533cf52de205e9e56c936c912dde6d8ee5c035cc/README.yaml index 60fe2ab3d0..3bbc580cfd 100644 --- a/Simulations/533/cf5/533cf52de205e9e56c936c912dde6d8ee5c035cc/533cf52de205e9e56c936c912dde6d8ee5c035cc/README.yaml +++ b/Simulations/533/cf5/533cf52de205e9e56c936c912dde6d8ee5c035cc/533cf52de205e9e56c936c912dde6d8ee5c035cc/README.yaml @@ -37,9 +37,12 @@ EXPERIMENT: - 10.1021/ja029029o/2 FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a SD5PC bilayer at 303.15 K (CHARMM36m, NAMD 3, 500 ns) [NMRlipids simulation 905] + name: Molecular dynamics trajectory of a SD5PC bilayer at 303.15 K (CHARMM36m, NAMD + 3, 500 ns) [NMRlipids simulation 905] alternateName: SDPC18:0(d35)/22:5n6PC) - description: Molecular dynamics trajectory of a lipid bilayer of 200 SD5PC (1-octadecanoyl-2-(4Z,7Z,10Z,13Z,16Z-docosapentaenoyl)-sn-glycero-3-phosphocholine) at 303.15 K. Simulated with CHARMM36m in NAMD 3 for 500 ns (57600 atoms). Deposited as NMRlipids Databank simulation 905 and available from https://doi.org/10.5281/zenodo.18470730. + description: Molecular dynamics trajectory of a lipid bilayer of 200 SD5PC (1-octadecanoyl-2-(4Z,7Z,10Z,13Z,16Z-docosapentaenoyl)-sn-glycero-3-phosphocholine) + at 303.15 K. Simulated with CHARMM36m in NAMD 3 for 500 ns (57600 atoms). Deposited + as NMRlipids Databank simulation 905 and available from https://doi.org/10.5281/zenodo.18470730. sameAs: https://doi.org/10.5281/zenodo.18470730 datePublished: '2026-02-03' license: @@ -130,7 +133,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.18470730 identifier: 10.5281/zenodo.18470730 url: https://doi.org/10.5281/zenodo.18470730 - name: 1-stearoyl(d35)-2-docosapentaenoyl-sn-glycero-3-phosphocholine (18:0(d35)/22:5n6PC) | SDPC lipid bilayer, 303K, CHARMM36m-WYF forcefield, NAMD 3.0.2, 2* 500 ns + name: 1-stearoyl(d35)-2-docosapentaenoyl-sn-glycero-3-phosphocholine (18:0(d35)/22:5n6PC) + | SDPC lipid bilayer, 303K, CHARMM36m-WYF forcefield, NAMD 3.0.2, 2* 500 ns publisher: Zenodo _source: api: datacite diff --git a/Simulations/539/765/5397656665e3e09c0a7c7d74bc10a0d5cee6c6e5/60c6a7e3acf926f35aa7223b6defe9763bde0140/README.yaml b/Simulations/539/765/5397656665e3e09c0a7c7d74bc10a0d5cee6c6e5/60c6a7e3acf926f35aa7223b6defe9763bde0140/README.yaml index c4bee9d0d6..ce158918b8 100644 --- a/Simulations/539/765/5397656665e3e09c0a7c7d74bc10a0d5cee6c6e5/60c6a7e3acf926f35aa7223b6defe9763bde0140/README.yaml +++ b/Simulations/539/765/5397656665e3e09c0a7c7d74bc10a0d5cee6c6e5/60c6a7e3acf926f35aa7223b6defe9763bde0140/README.yaml @@ -45,9 +45,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 264 bioschema_properties: - name: Molecular dynamics trajectory of a DOPE bilayer at 271 K (Berger-DOPE-2018, GROMACS 4.0.7, 200 ns) [NMRlipids simulation 264] + name: Molecular dynamics trajectory of a DOPE bilayer at 271 K (Berger-DOPE-2018, + GROMACS 4.0.7, 200 ns) [NMRlipids simulation 264] alternateName: 128DOPE_4789SOL_271K_v1 - description: Molecular dynamics trajectory of a lipid bilayer of 128 DOPE (1,2-dioleoyl-sn-glycero-3-phosphoethanolamine) at 271 K. Simulated with Berger-DOPE-2018 in GROMACS 4.0.7 for 200 ns (21279 atoms). Deposited as NMRlipids Databank simulation 264 and available from https://doi.org/10.5281/zenodo.1293905. + description: Molecular dynamics trajectory of a lipid bilayer of 128 DOPE (1,2-dioleoyl-sn-glycero-3-phosphoethanolamine) + at 271 K. Simulated with Berger-DOPE-2018 in GROMACS 4.0.7 for 200 ns (21279 atoms). + Deposited as NMRlipids Databank simulation 264 and available from https://doi.org/10.5281/zenodo.1293905. sameAs: https://doi.org/10.5281/zenodo.1293905 datePublished: '2018-06-20' license: diff --git a/Simulations/541/330/5413300b630cb69d17ee32f37bd904621cc091ec/3ef4a4a56814d7c1d1ed6dedb78cfb21d63e98f1/README.yaml b/Simulations/541/330/5413300b630cb69d17ee32f37bd904621cc091ec/3ef4a4a56814d7c1d1ed6dedb78cfb21d63e98f1/README.yaml index b22586e9cd..f48baa3754 100644 --- a/Simulations/541/330/5413300b630cb69d17ee32f37bd904621cc091ec/3ef4a4a56814d7c1d1ed6dedb78cfb21d63e98f1/README.yaml +++ b/Simulations/541/330/5413300b630cb69d17ee32f37bd904621cc091ec/3ef4a4a56814d7c1d1ed6dedb78cfb21d63e98f1/README.yaml @@ -49,9 +49,12 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/1 ID: 831 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 298 K (C36_Slipids_Hybrid, GROMACS 2024.3, 500 ns) [NMRlipids simulation 831] + name: Molecular dynamics trajectory of a POPC bilayer at 298 K (C36_Slipids_Hybrid, + GROMACS 2024.3, 500 ns) [NMRlipids simulation 831] alternateName: POPC_hybrid_slmdp - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 298 K. Simulated with C36_Slipids_Hybrid in GROMACS 2024.3 for 500 ns (36352 atoms). Deposited as NMRlipids Databank simulation 831 and available from https://doi.org/10.5281/zenodo.15172176. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 298 K. Simulated with C36_Slipids_Hybrid in GROMACS 2024.3 for 500 ns (36352 + atoms). Deposited as NMRlipids Databank simulation 831 and available from https://doi.org/10.5281/zenodo.15172176. sameAs: https://doi.org/10.5281/zenodo.15172176 datePublished: '2025-04-08' license: diff --git a/Simulations/542/36a/54236aa111e4179c44a16fc49d2612f32adaeb3c/dd67a93d52c6e2c67138fc0b7df85c12da774d6f/README.yaml b/Simulations/542/36a/54236aa111e4179c44a16fc49d2612f32adaeb3c/dd67a93d52c6e2c67138fc0b7df85c12da774d6f/README.yaml index 089f5c3fcd..82a8edf899 100644 --- a/Simulations/542/36a/54236aa111e4179c44a16fc49d2612f32adaeb3c/dd67a93d52c6e2c67138fc0b7df85c12da774d6f/README.yaml +++ b/Simulations/542/36a/54236aa111e4179c44a16fc49d2612f32adaeb3c/dd67a93d52c6e2c67138fc0b7df85c12da774d6f/README.yaml @@ -42,9 +42,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 713 bioschema_properties: - name: Molecular dynamics trajectory of a SOPC bilayer at 298.15 K (CHARMM36, GROMACS 2021, 1001 ns) [NMRlipids simulation 713] + name: Molecular dynamics trajectory of a SOPC bilayer at 298.15 K (CHARMM36, GROMACS + 2021, 1001 ns) [NMRlipids simulation 713] alternateName: SOPC_L - description: Molecular dynamics trajectory of a lipid bilayer of 1024 SOPC (1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 298.15 K. Simulated with CHARMM36 in GROMACS 2021 for 1001 ns (296960 atoms). Deposited as NMRlipids Databank simulation 713 and available from https://doi.org/10.5281/zenodo.7103807. + description: Molecular dynamics trajectory of a lipid bilayer of 1024 SOPC (1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 298.15 K. Simulated with CHARMM36 in GROMACS 2021 for 1001 ns (296960 atoms). + Deposited as NMRlipids Databank simulation 713 and available from https://doi.org/10.5281/zenodo.7103807. sameAs: https://doi.org/10.5281/zenodo.7103807 datePublished: '2022-09-22' license: diff --git a/Simulations/543/ab3/543ab3c1266ace288f9b39ed561851dfcbf5746d/fa7f266129d60fe835af632f66de4d1cd594b5e5/README.yaml b/Simulations/543/ab3/543ab3c1266ace288f9b39ed561851dfcbf5746d/fa7f266129d60fe835af632f66de4d1cd594b5e5/README.yaml index e14586a354..f6b9fa6e56 100644 --- a/Simulations/543/ab3/543ab3c1266ace288f9b39ed561851dfcbf5746d/fa7f266129d60fe835af632f66de4d1cd594b5e5/README.yaml +++ b/Simulations/543/ab3/543ab3c1266ace288f9b39ed561851dfcbf5746d/fa7f266129d60fe835af632f66de4d1cd594b5e5/README.yaml @@ -56,9 +56,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 408 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/SOD/CLA/POPS (47:26:17:9) bilayer at 298 K (CHARMM36, GROMACS, 200 ns) [NMRlipids simulation 408] + name: Molecular dynamics trajectory of a POPC/SOD/CLA/POPS (47:26:17:9) bilayer + at 298 K (CHARMM36, GROMACS, 200 ns) [NMRlipids simulation 408] alternateName: 110POPC_22POPS_4965SOL_61SOD_39CLA_298K - description: Molecular dynamics trajectory of a lipid bilayer of 110 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 47 mol%), 61 SOD (26 mol%), 39 CLA (17 mol%) and 22 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 9 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for 200 ns (32529 atoms). Deposited as NMRlipids Databank simulation 408 and available from https://doi.org/10.5281/zenodo.1493190. + description: Molecular dynamics trajectory of a lipid bilayer of 110 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 47 mol%), 61 SOD (26 mol%), 39 CLA (17 mol%) and 22 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, + 9 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for 200 ns (32529 atoms). + Deposited as NMRlipids Databank simulation 408 and available from https://doi.org/10.5281/zenodo.1493190. sameAs: https://doi.org/10.5281/zenodo.1493190 datePublished: '2018-11-21' license: diff --git a/Simulations/548/da1/548da10c309471a9611ac50e647b78d19df4cd40/40904384f62861b68749ab4f270a54491fe04f6f/README.yaml b/Simulations/548/da1/548da10c309471a9611ac50e647b78d19df4cd40/40904384f62861b68749ab4f270a54491fe04f6f/README.yaml index 2e550086b6..bc383336cf 100644 --- a/Simulations/548/da1/548da10c309471a9611ac50e647b78d19df4cd40/40904384f62861b68749ab4f270a54491fe04f6f/README.yaml +++ b/Simulations/548/da1/548da10c309471a9611ac50e647b78d19df4cd40/40904384f62861b68749ab4f270a54491fe04f6f/README.yaml @@ -67,9 +67,15 @@ EXPERIMENT: SAPI25: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POT/CLA/CHOL/SAPI25 (59:23:8:7:4) bilayer at 298.15 K (CHARMM36m, GROMACS 2020.1, 1204 ns) [NMRlipids simulation 785] + name: Molecular dynamics trajectory of a POPC/POT/CLA/CHOL/SAPI25 (59:23:8:7:4) + bilayer at 298.15 K (CHARMM36m, GROMACS 2020.1, 1204 ns) [NMRlipids simulation + 785] alternateName: POPC_254_SAPI25_16_CHOL_30_KCl_150mM_298.15K - description: Molecular dynamics trajectory of a lipid bilayer of 254 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 59 mol%), 97 POT (23 mol%), 33 CLA (8 mol%), 30 CHOL (cholesterol, 7 mol%) and 16 SAPI25 (1-stearoyl-2-arachidonoyl-sn-phosphatidylinositol 4,5-biphosphate, 4 mol%) at 298.15 K. Simulated with CHARMM36m in GROMACS 2020.1 for 1204 ns (76898 atoms). Deposited as NMRlipids Databank simulation 785 and available from https://doi.org/10.5281/zenodo.8370434. + description: Molecular dynamics trajectory of a lipid bilayer of 254 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 59 mol%), 97 POT (23 mol%), 33 CLA (8 mol%), 30 CHOL (cholesterol, 7 mol%) and + 16 SAPI25 (1-stearoyl-2-arachidonoyl-sn-phosphatidylinositol 4,5-biphosphate, + 4 mol%) at 298.15 K. Simulated with CHARMM36m in GROMACS 2020.1 for 1204 ns (76898 + atoms). Deposited as NMRlipids Databank simulation 785 and available from https://doi.org/10.5281/zenodo.8370434. sameAs: https://doi.org/10.5281/zenodo.8370434 datePublished: '2023-09-22' license: diff --git a/Simulations/549/7c7/5497c72e84f8a1d8895cf012fd0ba5e2dbb218f0/e689bf23a1b93998fb38f215c26871379a05247a/README.yaml b/Simulations/549/7c7/5497c72e84f8a1d8895cf012fd0ba5e2dbb218f0/e689bf23a1b93998fb38f215c26871379a05247a/README.yaml index fe25f7cec1..e014eb7a6f 100644 --- a/Simulations/549/7c7/5497c72e84f8a1d8895cf012fd0ba5e2dbb218f0/e689bf23a1b93998fb38f215c26871379a05247a/README.yaml +++ b/Simulations/549/7c7/5497c72e84f8a1d8895cf012fd0ba5e2dbb218f0/e689bf23a1b93998fb38f215c26871379a05247a/README.yaml @@ -52,9 +52,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 505 bioschema_properties: - name: Molecular dynamics trajectory of a POPE/POPG/SOD (60:20:20) bilayer at 310 K (Lipid17 for lipids and AMBER ff15ipq for ions, GROMACS 2018.3, 100 ns) [NMRlipids simulation 505] + name: Molecular dynamics trajectory of a POPE/POPG/SOD (60:20:20) bilayer at 310 + K (Lipid17 for lipids and AMBER ff15ipq for ions, GROMACS 2018.3, 100 ns) [NMRlipids + simulation 505] alternateName: POPE_POPG_SOD_SOL_310K - description: Molecular dynamics trajectory of a lipid bilayer of 374 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 60 mol%), 126 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 20 mol%) and 126 SOD (20 mol%) at 310 K. Simulated with Lipid17 for lipids and AMBER ff15ipq for ions in GROMACS 2018.3 for 100 ns (137878 atoms). Deposited as NMRlipids Databank simulation 505 and available from https://doi.org/10.5281/zenodo.3241269. + description: Molecular dynamics trajectory of a lipid bilayer of 374 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, + 60 mol%), 126 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 20 mol%) + and 126 SOD (20 mol%) at 310 K. Simulated with Lipid17 for lipids and AMBER ff15ipq + for ions in GROMACS 2018.3 for 100 ns (137878 atoms). Deposited as NMRlipids Databank + simulation 505 and available from https://doi.org/10.5281/zenodo.3241269. sameAs: https://doi.org/10.5281/zenodo.3241269 datePublished: '2019-06-07' license: diff --git a/Simulations/54b/650/54b6503812c7cd81137b04d302569bcd08aca03b/b56c1f05e72a73558cf1a7ac399a8420648399be/README.yaml b/Simulations/54b/650/54b6503812c7cd81137b04d302569bcd08aca03b/b56c1f05e72a73558cf1a7ac399a8420648399be/README.yaml index 07aeeac855..750f47c8cf 100644 --- a/Simulations/54b/650/54b6503812c7cd81137b04d302569bcd08aca03b/b56c1f05e72a73558cf1a7ac399a8420648399be/README.yaml +++ b/Simulations/54b/650/54b6503812c7cd81137b04d302569bcd08aca03b/b56c1f05e72a73558cf1a7ac399a8420648399be/README.yaml @@ -44,9 +44,12 @@ WARNINGS: PBC: z-jumps ID: 533 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 303 K (CHARMM36, GROMACS 4.5, 20 ns) [NMRlipids simulation 533] + name: Molecular dynamics trajectory of a POPC bilayer at 303 K (CHARMM36, GROMACS + 4.5, 20 ns) [NMRlipids simulation 533] alternateName: 72POPC_2242SOL_303K - description: Molecular dynamics trajectory of a lipid bilayer of 72 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 303 K. Simulated with CHARMM36 in GROMACS 4.5 for 20 ns (16374 atoms). Deposited as NMRlipids Databank simulation 533 and available from https://doi.org/10.5281/zenodo.13944. + description: Molecular dynamics trajectory of a lipid bilayer of 72 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 303 K. Simulated with CHARMM36 in GROMACS 4.5 for 20 ns (16374 atoms). Deposited + as NMRlipids Databank simulation 533 and available from https://doi.org/10.5281/zenodo.13944. sameAs: https://doi.org/10.5281/zenodo.13944 datePublished: '2015-01-14' license: @@ -137,7 +140,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.13944 identifier: 10.5281/zenodo.13944 url: https://doi.org/10.5281/zenodo.13944 - name: Md Simulation Trajectory And Related Files For Popc Bilayer (Charmm36, Gromacs 4.5) + name: Md Simulation Trajectory And Related Files For Popc Bilayer (Charmm36, Gromacs + 4.5) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/54e/467/54e46789de6e582fdb70695fbebbc9863311840a/d67a5e3538f0162fe43cb38d89f5e1b9ed136faa/README.yaml b/Simulations/54e/467/54e46789de6e582fdb70695fbebbc9863311840a/d67a5e3538f0162fe43cb38d89f5e1b9ed136faa/README.yaml index 124aceaaa0..8155796a46 100644 --- a/Simulations/54e/467/54e46789de6e582fdb70695fbebbc9863311840a/d67a5e3538f0162fe43cb38d89f5e1b9ed136faa/README.yaml +++ b/Simulations/54e/467/54e46789de6e582fdb70695fbebbc9863311840a/d67a5e3538f0162fe43cb38d89f5e1b9ed136faa/README.yaml @@ -49,9 +49,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 583 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (70:30) bilayer at 310 K (Slipids, GROMACS 4.6, 500 ns) [NMRlipids simulation 583] + name: Molecular dynamics trajectory of a POPC/CHOL (70:30) bilayer at 310 K (Slipids, + GROMACS 4.6, 500 ns) [NMRlipids simulation 583] alternateName: 200POPC_9000SOL_86CHOL_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 70 mol%) and 86 CHOL (cholesterol, 30 mol%) at 310 K. Simulated with Slipids in GROMACS 4.6 for 500 ns (60164 atoms). Deposited as NMRlipids Databank simulation 583 and available from https://doi.org/10.5281/zenodo.3243328. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 70 mol%) and 86 CHOL (cholesterol, 30 mol%) at 310 K. Simulated with Slipids in + GROMACS 4.6 for 500 ns (60164 atoms). Deposited as NMRlipids Databank simulation + 583 and available from https://doi.org/10.5281/zenodo.3243328. sameAs: https://doi.org/10.5281/zenodo.3243328 datePublished: '2016-08-22' license: @@ -140,7 +144,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3243328 identifier: 10.5281/zenodo.3243328 url: https://doi.org/10.5281/zenodo.3243328 - name: POPC with 0, 10, 20, and 30 mol-% of cholesterol at 310 K. Slipids force field. + name: POPC with 0, 10, 20, and 30 mol-% of cholesterol at 310 K. Slipids force + field. publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/558/c0a/558c0a75d0bc353ecff2826dccac563abf5ac695/bd9ca461ab75b6821c83b5337dc6c8d3a6de37b4/README.yaml b/Simulations/558/c0a/558c0a75d0bc353ecff2826dccac563abf5ac695/bd9ca461ab75b6821c83b5337dc6c8d3a6de37b4/README.yaml index f0e8e15f0e..b4d12aaf9b 100644 --- a/Simulations/558/c0a/558c0a75d0bc353ecff2826dccac563abf5ac695/bd9ca461ab75b6821c83b5337dc6c8d3a6de37b4/README.yaml +++ b/Simulations/558/c0a/558c0a75d0bc353ecff2826dccac563abf5ac695/bd9ca461ab75b6821c83b5337dc6c8d3a6de37b4/README.yaml @@ -53,9 +53,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/9 ID: 714 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (53:47) bilayer at 298.15 K (Lipid17, GROMACS 2021, 1001 ns) [NMRlipids simulation 714] + name: Molecular dynamics trajectory of a POPC/CHOL (53:47) bilayer at 298.15 K (Lipid17, + GROMACS 2021, 1001 ns) [NMRlipids simulation 714] alternateName: Lipid17_POPC_CHOL47_M - description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 53 mol%) and 224 CHOL (cholesterol, 47 mol%) at 298.15 K. Simulated with Lipid17 in GROMACS 2021 for 1001 ns (122880 atoms). Deposited as NMRlipids Databank simulation 714 and available from https://doi.org/10.5281/zenodo.6992065. + description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 53 mol%) and 224 CHOL (cholesterol, 47 mol%) at 298.15 K. Simulated with Lipid17 + in GROMACS 2021 for 1001 ns (122880 atoms). Deposited as NMRlipids Databank simulation + 714 and available from https://doi.org/10.5281/zenodo.6992065. sameAs: https://doi.org/10.5281/zenodo.6992065 datePublished: '2022-08-15' license: diff --git a/Simulations/562/3a4/5623a4321f64219cfae8f12ec127db17406519a5/44e83a419d30e168df92735a26b23caeac357178/README.yaml b/Simulations/562/3a4/5623a4321f64219cfae8f12ec127db17406519a5/44e83a419d30e168df92735a26b23caeac357178/README.yaml index 64d7dc8b42..42af66b542 100644 --- a/Simulations/562/3a4/5623a4321f64219cfae8f12ec127db17406519a5/44e83a419d30e168df92735a26b23caeac357178/README.yaml +++ b/Simulations/562/3a4/5623a4321f64219cfae8f12ec127db17406519a5/44e83a419d30e168df92735a26b23caeac357178/README.yaml @@ -39,9 +39,13 @@ DATEOFRUNNING: '2026-09-17' TYPEOFSYSTEM: lipid bilayer ID: 937 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC bilayer at 327 K (prosECCo 75 paper related data, GROMACS 2022.5-plumed_2.8.2, 1000 ns) [NMRlipids simulation -1] + name: Molecular dynamics trajectory of a DPPC bilayer at 327 K (prosECCo 75 paper + related data, GROMACS 2022.5-plumed_2.8.2, 1000 ns) [NMRlipids simulation -1] alternateName: DPPC_200_SOL_9000_prosECCo75_LO_327K - description: Molecular dynamics trajectory of a lipid bilayer of 200 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) at 327 K. Simulated with prosECCo 75 paper related data in GROMACS 2022.5-plumed_2.8.2 for 1000 ns (53000 atoms). Deposited as NMRlipids Databank simulation -1 and available from https://doi.org/10.5281/zenodo.10635500. + description: Molecular dynamics trajectory of a lipid bilayer of 200 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) + at 327 K. Simulated with prosECCo 75 paper related data in GROMACS 2022.5-plumed_2.8.2 + for 1000 ns (53000 atoms). Deposited as NMRlipids Databank simulation -1 and available + from https://doi.org/10.5281/zenodo.10635500. sameAs: https://doi.org/10.5281/zenodo.10635500 datePublished: '2024-02-08' license: @@ -137,3 +141,7 @@ bioschema_properties: doi: 10.5281/zenodo.10635500 spdxLicenseList: 3.29.0 retrieved: '2026-09-22' +EXPERIMENT: + ORDERPARAMETER: + DPPC: [] + FORMFACTOR: [] diff --git a/Simulations/565/778/5657789464985793910172f7b59e29a74d19c77c/272f4bf2e18e4341e93ca1434079bb49cf6245cd/README.yaml b/Simulations/565/778/5657789464985793910172f7b59e29a74d19c77c/272f4bf2e18e4341e93ca1434079bb49cf6245cd/README.yaml index 2b1ab041cf..bd70a53571 100644 --- a/Simulations/565/778/5657789464985793910172f7b59e29a74d19c77c/272f4bf2e18e4341e93ca1434079bb49cf6245cd/README.yaml +++ b/Simulations/565/778/5657789464985793910172f7b59e29a74d19c77c/272f4bf2e18e4341e93ca1434079bb49cf6245cd/README.yaml @@ -45,9 +45,12 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/1 ID: 715 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 298.15 K (Lipid17, GROMACS 2021, 1001 ns) [NMRlipids simulation 715] + name: Molecular dynamics trajectory of a POPC bilayer at 298.15 K (Lipid17, GROMACS + 2021, 1001 ns) [NMRlipids simulation 715] alternateName: Lipid17_POPC_S - description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 298.15 K. Simulated with Lipid17 in GROMACS 2021 for 1001 ns (18176 atoms). Deposited as NMRlipids Databank simulation 715 and available from https://doi.org/10.5281/zenodo.6992065. + description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 298.15 K. Simulated with Lipid17 in GROMACS 2021 for 1001 ns (18176 atoms). + Deposited as NMRlipids Databank simulation 715 and available from https://doi.org/10.5281/zenodo.6992065. sameAs: https://doi.org/10.5281/zenodo.6992065 datePublished: '2022-08-15' license: diff --git a/Simulations/568/5fe/5685fec84c6595c5a4242b41a9e79ac6e67dfefb/41de202addf945cd61cfdf1537d775af00adc37b/README.yaml b/Simulations/568/5fe/5685fec84c6595c5a4242b41a9e79ac6e67dfefb/41de202addf945cd61cfdf1537d775af00adc37b/README.yaml index cc776279d2..c483968c4a 100644 --- a/Simulations/568/5fe/5685fec84c6595c5a4242b41a9e79ac6e67dfefb/41de202addf945cd61cfdf1537d775af00adc37b/README.yaml +++ b/Simulations/568/5fe/5685fec84c6595c5a4242b41a9e79ac6e67dfefb/41de202addf945cd61cfdf1537d775af00adc37b/README.yaml @@ -51,9 +51,13 @@ EXPERIMENT: CHOL: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a DOPC/CHOL (71:29) bilayer at 333.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 651] + name: Molecular dynamics trajectory of a DOPC/CHOL (71:29) bilayer at 333.15 K (CHARMM36, + GROMACS, 1001 ns) [NMRlipids simulation 651] alternateName: 256DOPC_104CHOL_18000SOL_333K - description: Molecular dynamics trajectory of a lipid bilayer of 256 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, 71 mol%) and 104 CHOL (cholesterol, 29 mol%) at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (97024 atoms). Deposited as NMRlipids Databank simulation 651 and available from https://doi.org/10.5281/zenodo.6943929. + description: Molecular dynamics trajectory of a lipid bilayer of 256 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, + 71 mol%) and 104 CHOL (cholesterol, 29 mol%) at 333.15 K. Simulated with CHARMM36 + in GROMACS for 1001 ns (97024 atoms). Deposited as NMRlipids Databank simulation + 651 and available from https://doi.org/10.5281/zenodo.6943929. sameAs: https://doi.org/10.5281/zenodo.6943929 datePublished: '2022-07-30' license: diff --git a/Simulations/568/efe/568efe83b7ac0fa45bd7b3cd683f43b571d13115/b766113b1bec2f3668be2c82812c23164c42eeea/README.yaml b/Simulations/568/efe/568efe83b7ac0fa45bd7b3cd683f43b571d13115/b766113b1bec2f3668be2c82812c23164c42eeea/README.yaml index 5863a529ff..dd6fd961b4 100644 --- a/Simulations/568/efe/568efe83b7ac0fa45bd7b3cd683f43b571d13115/b766113b1bec2f3668be2c82812c23164c42eeea/README.yaml +++ b/Simulations/568/efe/568efe83b7ac0fa45bd7b3cd683f43b571d13115/b766113b1bec2f3668be2c82812c23164c42eeea/README.yaml @@ -51,9 +51,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/8 ID: 716 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (62:38) bilayer at 298.15 K (MacRog, GROMACS 2021, 1001 ns) [NMRlipids simulation 716] + name: Molecular dynamics trajectory of a POPC/CHOL (62:38) bilayer at 298.15 K (MacRog, + GROMACS 2021, 1001 ns) [NMRlipids simulation 716] alternateName: MacRog_POPC_CHOL38_S - description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 62 mol%) and 40 CHOL (cholesterol, 38 mol%) at 298.15 K. Simulated with MacRog in GROMACS 2021 for 1001 ns (27136 atoms). Deposited as NMRlipids Databank simulation 716 and available from https://doi.org/10.5281/zenodo.7061800. + description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 62 mol%) and 40 CHOL (cholesterol, 38 mol%) at 298.15 K. Simulated with MacRog + in GROMACS 2021 for 1001 ns (27136 atoms). Deposited as NMRlipids Databank simulation + 716 and available from https://doi.org/10.5281/zenodo.7061800. sameAs: https://doi.org/10.5281/zenodo.7061800 datePublished: '2022-09-08' license: diff --git a/Simulations/569/9d1/5699d1a111be55a0836ac0d14c05f5dbe299ad4f/8512456873921bf00c5c85fe78a412585dd437c3/README.yaml b/Simulations/569/9d1/5699d1a111be55a0836ac0d14c05f5dbe299ad4f/8512456873921bf00c5c85fe78a412585dd437c3/README.yaml index 3853cd7ac2..d3a7c56e5b 100644 --- a/Simulations/569/9d1/5699d1a111be55a0836ac0d14c05f5dbe299ad4f/8512456873921bf00c5c85fe78a412585dd437c3/README.yaml +++ b/Simulations/569/9d1/5699d1a111be55a0836ac0d14c05f5dbe299ad4f/8512456873921bf00c5c85fe78a412585dd437c3/README.yaml @@ -49,9 +49,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 397 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (84:8:8) bilayer at 298.15 K (Lipid14 for lipids and AMBER99SB-ILDN for ions, GROMACS 5.0.3, 100 ns) [NMRlipids simulation 397] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (84:8:8) bilayer at 298.15 + K (Lipid14 for lipids and AMBER99SB-ILDN for ions, GROMACS 5.0.3, 100 ns) [NMRlipids + simulation 397] alternateName: 128POPC_5120SOL_12SOD_12CLA_298K - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 84 mol%), 12 CLA (8 mol%) and 12 SOD (8 mol%) at 298.15 K. Simulated with Lipid14 for lipids and AMBER99SB-ILDN for ions in GROMACS 5.0.3 for 100 ns (32536 atoms). Deposited as NMRlipids Databank simulation 397 and available from https://doi.org/10.5281/zenodo.30891. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 84 mol%), 12 CLA (8 mol%) and 12 SOD (8 mol%) at 298.15 K. Simulated with Lipid14 + for lipids and AMBER99SB-ILDN for ions in GROMACS 5.0.3 for 100 ns (32536 atoms). + Deposited as NMRlipids Databank simulation 397 and available from https://doi.org/10.5281/zenodo.30891. sameAs: https://doi.org/10.5281/zenodo.30891 datePublished: '2015-09-11' license: diff --git a/Simulations/56c/4ef/56c4ef96aa5c69d83e29931530671e25d8f6c700/b5c8e3f2998e01392bea661eea88bebed3439913/README.yaml b/Simulations/56c/4ef/56c4ef96aa5c69d83e29931530671e25d8f6c700/b5c8e3f2998e01392bea661eea88bebed3439913/README.yaml index 8bc2c19baa..b1ee366c0c 100644 --- a/Simulations/56c/4ef/56c4ef96aa5c69d83e29931530671e25d8f6c700/b5c8e3f2998e01392bea661eea88bebed3439913/README.yaml +++ b/Simulations/56c/4ef/56c4ef96aa5c69d83e29931530671e25d8f6c700/b5c8e3f2998e01392bea661eea88bebed3439913/README.yaml @@ -51,9 +51,13 @@ EXPERIMENT: GB3: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD/GB3 (75:11:11:4) bilayer at 310 K (CHARMM36m, GROMACS 2019.4/2020, 7250 ns) [NMRlipids simulation 851] + name: Molecular dynamics trajectory of a POPC/CLA/SOD/GB3 (75:11:11:4) bilayer at + 310 K (CHARMM36m, GROMACS 2019.4/2020, 7250 ns) [NMRlipids simulation 851] alternateName: POPC:Gb3_run2(95:5 mol:mol) - description: Molecular dynamics trajectory of a lipid bilayer of 190 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 75 mol%), 27 CLA (11 mol%), 27 SOD (11 mol%) and 10 GB3 (Gb3(d18:1/24:0), 4 mol%) at 310 K. Simulated with CHARMM36m in GROMACS 2019.4/2020 for 7250 ns (74381 atoms). Deposited as NMRlipids Databank simulation 851 and available from https://doi.org/10.5281/zenodo.10635875. + description: Molecular dynamics trajectory of a lipid bilayer of 190 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 75 mol%), 27 CLA (11 mol%), 27 SOD (11 mol%) and 10 GB3 (Gb3(d18:1/24:0), 4 mol%) + at 310 K. Simulated with CHARMM36m in GROMACS 2019.4/2020 for 7250 ns (74381 atoms). + Deposited as NMRlipids Databank simulation 851 and available from https://doi.org/10.5281/zenodo.10635875. sameAs: https://doi.org/10.5281/zenodo.10635875 datePublished: '2024-02-08' license: diff --git a/Simulations/56d/a13/56da13d75083be31f883218a786e0e9fe747d171/7c69a0cd5b74f858cab17714cb172bfe8c8d63d8/README.yaml b/Simulations/56d/a13/56da13d75083be31f883218a786e0e9fe747d171/7c69a0cd5b74f858cab17714cb172bfe8c8d63d8/README.yaml index 3acdfd47e9..a061fab2ae 100644 --- a/Simulations/56d/a13/56da13d75083be31f883218a786e0e9fe747d171/7c69a0cd5b74f858cab17714cb172bfe8c8d63d8/README.yaml +++ b/Simulations/56d/a13/56da13d75083be31f883218a786e0e9fe747d171/7c69a0cd5b74f858cab17714cb172bfe8c8d63d8/README.yaml @@ -55,9 +55,13 @@ EXPERIMENT: POPE: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a POPE/NH4/POPI (43:29:29) bilayer at 310 K (CHARMM36, GROMACS 2022.4, 500 ns) [NMRlipids simulation 853] + name: Molecular dynamics trajectory of a POPE/NH4/POPI (43:29:29) bilayer at 310 + K (CHARMM36, GROMACS 2022.4, 500 ns) [NMRlipids simulation 853] alternateName: POPI-POPE (40:60), full hydration, 310 K, NH4+ counter ions - description: Molecular dynamics trajectory of a lipid bilayer of 120 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 43 mol%), 80 NH4 (29 mol%) and 80 POPI (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoinositol, 29 mol%) at 310 K. Simulated with CHARMM36 in GROMACS 2022.4 for 500 ns (56360 atoms). Deposited as NMRlipids Databank simulation 853 and available from https://doi.org/10.5281/zenodo.10261345. + description: Molecular dynamics trajectory of a lipid bilayer of 120 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, + 43 mol%), 80 NH4 (29 mol%) and 80 POPI (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoinositol, + 29 mol%) at 310 K. Simulated with CHARMM36 in GROMACS 2022.4 for 500 ns (56360 + atoms). Deposited as NMRlipids Databank simulation 853 and available from https://doi.org/10.5281/zenodo.10261345. sameAs: https://doi.org/10.5281/zenodo.10261345 datePublished: '2023-12-18' license: diff --git a/Simulations/571/d0a/571d0aa14fceb25aeb6a14639fff996618abdc01/02b4649fc34c5474f700cc9900d56e64ad4fe43d/README.yaml b/Simulations/571/d0a/571d0aa14fceb25aeb6a14639fff996618abdc01/02b4649fc34c5474f700cc9900d56e64ad4fe43d/README.yaml index 656b925dee..1a91e17bf7 100644 --- a/Simulations/571/d0a/571d0aa14fceb25aeb6a14639fff996618abdc01/02b4649fc34c5474f700cc9900d56e64ad4fe43d/README.yaml +++ b/Simulations/571/d0a/571d0aa14fceb25aeb6a14639fff996618abdc01/02b4649fc34c5474f700cc9900d56e64ad4fe43d/README.yaml @@ -50,9 +50,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 54 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (84:8:8) bilayer at 310 K (Slipids, GROMACS 5.1.2, 100 ns) [NMRlipids simulation 54] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (84:8:8) bilayer at 310 K + (Slipids, GROMACS 5.1.2, 100 ns) [NMRlipids simulation 54] alternateName: 500POPC_25000SOL_48SOD_48CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 500 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 84 mol%), 48 CLA (8 mol%) and 48 SOD (8 mol%) at 310 K. Simulated with Slipids in GROMACS 5.1.2 for 100 ns (142096 atoms). Deposited as NMRlipids Databank simulation 54 and available from https://doi.org/10.5281/zenodo.2574689. + description: Molecular dynamics trajectory of a lipid bilayer of 500 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 84 mol%), 48 CLA (8 mol%) and 48 SOD (8 mol%) at 310 K. Simulated with Slipids + in GROMACS 5.1.2 for 100 ns (142096 atoms). Deposited as NMRlipids Databank simulation + 54 and available from https://doi.org/10.5281/zenodo.2574689. sameAs: https://doi.org/10.5281/zenodo.2574689 datePublished: '2019-02-21' license: diff --git a/Simulations/572/038/57203893c96a9a1ff45aa175de11da7e9ef8b826/30a1dfaac4a4342e6d59f56b77614b375b4f96c0/README.yaml b/Simulations/572/038/57203893c96a9a1ff45aa175de11da7e9ef8b826/30a1dfaac4a4342e6d59f56b77614b375b4f96c0/README.yaml index e1a4a7d846..a6b45d250f 100644 --- a/Simulations/572/038/57203893c96a9a1ff45aa175de11da7e9ef8b826/30a1dfaac4a4342e6d59f56b77614b375b4f96c0/README.yaml +++ b/Simulations/572/038/57203893c96a9a1ff45aa175de11da7e9ef8b826/30a1dfaac4a4342e6d59f56b77614b375b4f96c0/README.yaml @@ -55,9 +55,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 228 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPS/SOD (83:8:8) bilayer at 298 K (ECC-lipids, SPC water model, ECC-ions, GROMACS 2018.0, 983 ns) [NMRlipids simulation 228] + name: Molecular dynamics trajectory of a POPC/POPS/SOD (83:8:8) bilayer at 298 K + (ECC-lipids, SPC water model, ECC-ions, GROMACS 2018.0, 983 ns) [NMRlipids simulation + 228] alternateName: 6POPS_60POPC_3600SOL_6SOD_298K_ECC-lipid - description: Molecular dynamics trajectory of a lipid bilayer of 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 83 mol%), 6 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 8 mol%) and 6 SOD (8 mol%) at 298 K. Simulated with ECC-lipids, SPC water model, ECC-ions in GROMACS 2018.0 for 983 ns (19608 atoms). Deposited as NMRlipids Databank simulation 228 and available from https://doi.org/10.5281/zenodo.1488094. + description: Molecular dynamics trajectory of a lipid bilayer of 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 83 mol%), 6 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 8 mol%) + and 6 SOD (8 mol%) at 298 K. Simulated with ECC-lipids, SPC water model, ECC-ions + in GROMACS 2018.0 for 983 ns (19608 atoms). Deposited as NMRlipids Databank simulation + 228 and available from https://doi.org/10.5281/zenodo.1488094. sameAs: https://doi.org/10.5281/zenodo.1488094 datePublished: '2018-11-14' license: @@ -148,7 +154,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1488094 identifier: 10.5281/zenodo.1488094 url: https://doi.org/10.5281/zenodo.1488094 - name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS (various mixtures) with ECC-lipids force field, and Na+ (K+) counterions + name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS + (various mixtures) with ECC-lipids force field, and Na+ (K+) counterions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/575/13b/57513b7ed199f77f6406c79e9c66316e555b66a5/915a33e59d398ef532541e7c1560a2da7a20a2ee/README.yaml b/Simulations/575/13b/57513b7ed199f77f6406c79e9c66316e555b66a5/915a33e59d398ef532541e7c1560a2da7a20a2ee/README.yaml index 11b6d3cad9..a1a2704119 100644 --- a/Simulations/575/13b/57513b7ed199f77f6406c79e9c66316e555b66a5/915a33e59d398ef532541e7c1560a2da7a20a2ee/README.yaml +++ b/Simulations/575/13b/57513b7ed199f77f6406c79e9c66316e555b66a5/915a33e59d398ef532541e7c1560a2da7a20a2ee/README.yaml @@ -45,9 +45,12 @@ EXPERIMENT: - 10.1021/acs.jpcb.4c04719/3 FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 300 K (CHARMM36, GROMACS 2022.4, 450 ns) [NMRlipids simulation 798] + name: Molecular dynamics trajectory of a POPC bilayer at 300 K (CHARMM36, GROMACS + 2022.4, 450 ns) [NMRlipids simulation 798] alternateName: 200POPC_2400SOL_300K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 300 K. Simulated with CHARMM36 in GROMACS 2022.4 for 450 ns (34000 atoms). Deposited as NMRlipids Databank simulation 798 and available from https://doi.org/10.5281/zenodo.10908936. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 300 K. Simulated with CHARMM36 in GROMACS 2022.4 for 450 ns (34000 atoms). + Deposited as NMRlipids Databank simulation 798 and available from https://doi.org/10.5281/zenodo.10908936. sameAs: https://doi.org/10.5281/zenodo.10908936 datePublished: '2024-04-02' license: diff --git a/Simulations/575/abb/575abbac27d285e5cd72dd30f79c53c89a2e383c/f4cae31a4921bccd6e8ede49f15861d2bba0f7a1/README.yaml b/Simulations/575/abb/575abbac27d285e5cd72dd30f79c53c89a2e383c/f4cae31a4921bccd6e8ede49f15861d2bba0f7a1/README.yaml index 6a74751a1a..dc21eefa60 100644 --- a/Simulations/575/abb/575abbac27d285e5cd72dd30f79c53c89a2e383c/f4cae31a4921bccd6e8ede49f15861d2bba0f7a1/README.yaml +++ b/Simulations/575/abb/575abbac27d285e5cd72dd30f79c53c89a2e383c/f4cae31a4921bccd6e8ede49f15861d2bba0f7a1/README.yaml @@ -50,9 +50,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 557 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (48:35:17) bilayer at 350 K (Slipids with ECC-scaled ions (Kohagen), GROMACS 4.6, 800 ns) [NMRlipids simulation 557] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (48:35:17) bilayer at 350 + K (Slipids with ECC-scaled ions (Kohagen), GROMACS 4.6, 800 ns) [NMRlipids simulation + 557] alternateName: 200POPC_9000SOL_73CAL_146CLA_350K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 48 mol%), 146 CLA (35 mol%) and 73 CAL (17 mol%) at 350 K. Simulated with Slipids with ECC-scaled ions (Kohagen) in GROMACS 4.6 for 800 ns (54019 atoms). Deposited as NMRlipids Databank simulation 557 and available from https://doi.org/10.5281/zenodo.259354. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 48 mol%), 146 CLA (35 mol%) and 73 CAL (17 mol%) at 350 K. Simulated with Slipids + with ECC-scaled ions (Kohagen) in GROMACS 4.6 for 800 ns (54019 atoms). Deposited + as NMRlipids Databank simulation 557 and available from https://doi.org/10.5281/zenodo.259354. sameAs: https://doi.org/10.5281/zenodo.259354 datePublished: '2017-01-24' license: @@ -140,7 +145,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.259354 identifier: 10.5281/zenodo.259354 url: https://doi.org/10.5281/zenodo.259354 - name: Popc With Varying Amounts Of Cholesterol, 450 Mm Of Cacl_2. Slipids With Ecc-Scaled Ions + name: Popc With Varying Amounts Of Cholesterol, 450 Mm Of Cacl_2. Slipids With + Ecc-Scaled Ions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/57b/0ad/57b0ad076b231fc7a937392165ea0c0a5bcf57e9/3a34b50be663922103f5db3ded6809fead76124b/README.yaml b/Simulations/57b/0ad/57b0ad076b231fc7a937392165ea0c0a5bcf57e9/3a34b50be663922103f5db3ded6809fead76124b/README.yaml index e21b62f19c..f71c539ed4 100644 --- a/Simulations/57b/0ad/57b0ad076b231fc7a937392165ea0c0a5bcf57e9/3a34b50be663922103f5db3ded6809fead76124b/README.yaml +++ b/Simulations/57b/0ad/57b0ad076b231fc7a937392165ea0c0a5bcf57e9/3a34b50be663922103f5db3ded6809fead76124b/README.yaml @@ -62,9 +62,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 300 bioschema_properties: - name: Molecular dynamics trajectory of a SOD/CLA/POPC/POPS (43:40:14:3) bilayer at 298 K (ECC-lipids, GROMACS 2018.0, 1000 ns) [NMRlipids simulation 300] + name: Molecular dynamics trajectory of a SOD/CLA/POPC/POPS (43:40:14:3) bilayer + at 298 K (ECC-lipids, GROMACS 2018.0, 1000 ns) [NMRlipids simulation 300] alternateName: 12POPS_60POPC_3213SOL_186SOD_174CLA_298K - description: Molecular dynamics trajectory of a lipid bilayer of 186 SOD (43 mol%), 174 CLA (40 mol%), 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 14 mol%) and 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 3 mol%) at 298 K. Simulated with ECC-lipids in GROMACS 2018.0 for 1000 ns (19563 atoms). Deposited as NMRlipids Databank simulation 300 and available from https://doi.org/10.5281/zenodo.3332778. + description: Molecular dynamics trajectory of a lipid bilayer of 186 SOD (43 mol%), + 174 CLA (40 mol%), 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 14 mol%) and 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 3 mol%) + at 298 K. Simulated with ECC-lipids in GROMACS 2018.0 for 1000 ns (19563 atoms). + Deposited as NMRlipids Databank simulation 300 and available from https://doi.org/10.5281/zenodo.3332778. sameAs: https://doi.org/10.5281/zenodo.3332778 datePublished: '2018-11-14' license: @@ -156,7 +161,9 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3332778 identifier: 10.5281/zenodo.3332778 url: https://doi.org/10.5281/zenodo.3332778 - name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS (5:1) with ECC-lipids force field, and Na+ (K+) counterions at various additional concentrations of NaCl and KCl + name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS + (5:1) with ECC-lipids force field, and Na+ (K+) counterions at various additional + concentrations of NaCl and KCl publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/57d/cf3/57dcf31921c5d93e27e791e370cc91a9942e33ac/e7f5255587705605fac69434923686b72700b8c5/README.yaml b/Simulations/57d/cf3/57dcf31921c5d93e27e791e370cc91a9942e33ac/e7f5255587705605fac69434923686b72700b8c5/README.yaml index 262e5122b4..837e421bf7 100644 --- a/Simulations/57d/cf3/57dcf31921c5d93e27e791e370cc91a9942e33ac/e7f5255587705605fac69434923686b72700b8c5/README.yaml +++ b/Simulations/57d/cf3/57dcf31921c5d93e27e791e370cc91a9942e33ac/e7f5255587705605fac69434923686b72700b8c5/README.yaml @@ -54,9 +54,13 @@ EXPERIMENT: BOG: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a BOG/DMPC (50:50) bilayer at 303.15 K (Charmm36, GROMACS 2023.2, 500 ns) [NMRlipids simulation 821] + name: Molecular dynamics trajectory of a BOG/DMPC (50:50) bilayer at 303.15 K (Charmm36, + GROMACS 2023.2, 500 ns) [NMRlipids simulation 821] alternateName: DMPC_BOG_1x1_fh - description: Molecular dynamics trajectory of a lipid bilayer of 90 BOG (beta-octyl D-glucopyranoside, 50 mol%) and 90 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine, 50 mol%) at 303.15 K. Simulated with Charmm36 in GROMACS 2023.2 for 500 ns (47046 atoms). Deposited as NMRlipids Databank simulation 821 and available from https://doi.org/10.5281/zenodo.13881447. + description: Molecular dynamics trajectory of a lipid bilayer of 90 BOG (beta-octyl + D-glucopyranoside, 50 mol%) and 90 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine, + 50 mol%) at 303.15 K. Simulated with Charmm36 in GROMACS 2023.2 for 500 ns (47046 + atoms). Deposited as NMRlipids Databank simulation 821 and available from https://doi.org/10.5281/zenodo.13881447. sameAs: https://doi.org/10.5281/zenodo.13881447 datePublished: '2024-10-02' license: diff --git a/Simulations/586/751/586751ac660876b4f4dfc6b4ccb21d2285ac2a9f/9835edfc64a50ef2ec61eaa555cbffc60e4bfabf/README.yaml b/Simulations/586/751/586751ac660876b4f4dfc6b4ccb21d2285ac2a9f/9835edfc64a50ef2ec61eaa555cbffc60e4bfabf/README.yaml index de8be93190..81369cef2c 100644 --- a/Simulations/586/751/586751ac660876b4f4dfc6b4ccb21d2285ac2a9f/9835edfc64a50ef2ec61eaa555cbffc60e4bfabf/README.yaml +++ b/Simulations/586/751/586751ac660876b4f4dfc6b4ccb21d2285ac2a9f/9835edfc64a50ef2ec61eaa555cbffc60e4bfabf/README.yaml @@ -54,9 +54,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 33 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (73:18:9) bilayer at 310.15 K (CHARMM36 NBFIX Kim, GROMACS, 432 ns) [NMRlipids simulation 33] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (73:18:9) bilayer at 310.15 + K (CHARMM36 NBFIX Kim, GROMACS, 432 ns) [NMRlipids simulation 33] alternateName: 200POPC_9000SOL_25CAL_50CLA_310K_NBFIXKim - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 73 mol%), 50 CLA (18 mol%) and 25 CAL (9 mol%) at 310.15 K. Simulated with CHARMM36 NBFIX Kim in GROMACS for 432 ns (53875 atoms). Deposited as NMRlipids Databank simulation 33 and available from https://doi.org/10.5281/zenodo.3434396. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 73 mol%), 50 CLA (18 mol%) and 25 CAL (9 mol%) at 310.15 K. Simulated with CHARMM36 + NBFIX Kim in GROMACS for 432 ns (53875 atoms). Deposited as NMRlipids Databank + simulation 33 and available from https://doi.org/10.5281/zenodo.3434396. sameAs: https://doi.org/10.5281/zenodo.3434396 datePublished: '2019-09-17' license: diff --git a/Simulations/589/27c/58927c60d9fa51b9edd458502c6858dd25cba6af/852e7682947b9bb47cb8e216540acaaa267b3b57/README.yaml b/Simulations/589/27c/58927c60d9fa51b9edd458502c6858dd25cba6af/852e7682947b9bb47cb8e216540acaaa267b3b57/README.yaml index a5d1544120..5cb830db07 100644 --- a/Simulations/589/27c/58927c60d9fa51b9edd458502c6858dd25cba6af/852e7682947b9bb47cb8e216540acaaa267b3b57/README.yaml +++ b/Simulations/589/27c/58927c60d9fa51b9edd458502c6858dd25cba6af/852e7682947b9bb47cb8e216540acaaa267b3b57/README.yaml @@ -40,9 +40,12 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/1 ID: 832 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 300 K (FF-development, GROMACS, 286 ns) [NMRlipids simulation 832] + name: Molecular dynamics trajectory of a POPC bilayer at 300 K (FF-development, + GROMACS, 286 ns) [NMRlipids simulation 832] alternateName: POPCandTIP3P - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 300 K. Simulated with FF-development in GROMACS for 286 ns (32512 atoms). Deposited as NMRlipids Databank simulation 832 and available from https://doi.org/10.5281/zenodo.15002712. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 300 K. Simulated with FF-development in GROMACS for 286 ns (32512 atoms). Deposited + as NMRlipids Databank simulation 832 and available from https://doi.org/10.5281/zenodo.15002712. sameAs: https://doi.org/10.5281/zenodo.15002712 datePublished: '2025-03-10' license: diff --git a/Simulations/58c/b75/58cb75736e26996a54df4e3b6c0fc2ba412947e7/4289a5cc193691837cd6051f696359db7e87ddbf/README.yaml b/Simulations/58c/b75/58cb75736e26996a54df4e3b6c0fc2ba412947e7/4289a5cc193691837cd6051f696359db7e87ddbf/README.yaml index 34b3e2eba8..fb0161bdaf 100644 --- a/Simulations/58c/b75/58cb75736e26996a54df4e3b6c0fc2ba412947e7/4289a5cc193691837cd6051f696359db7e87ddbf/README.yaml +++ b/Simulations/58c/b75/58cb75736e26996a54df4e3b6c0fc2ba412947e7/4289a5cc193691837cd6051f696359db7e87ddbf/README.yaml @@ -44,9 +44,12 @@ EXPERIMENT: DYPC: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a DYPC bilayer at 333.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 638] + name: Molecular dynamics trajectory of a DYPC bilayer at 333.15 K (CHARMM36, GROMACS, + 1001 ns) [NMRlipids simulation 638] alternateName: 256DYPC_12800SOL_333K - description: Molecular dynamics trajectory of a lipid bilayer of 256 DYPC (1,2-(16:1$^\Delta9$)-sn-glycero-3-phosphocholine) at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (70656 atoms). Deposited as NMRlipids Databank simulation 638 and available from https://doi.org/10.5281/zenodo.6943413. + description: Molecular dynamics trajectory of a lipid bilayer of 256 DYPC (1,2-(16:1$^\Delta9$)-sn-glycero-3-phosphocholine) + at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (70656 atoms). Deposited + as NMRlipids Databank simulation 638 and available from https://doi.org/10.5281/zenodo.6943413. sameAs: https://doi.org/10.5281/zenodo.6943413 datePublished: '2022-07-30' license: @@ -134,7 +137,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.6943413 identifier: 10.5281/zenodo.6943413 url: https://doi.org/10.5281/zenodo.6943413 - name: Simulations of different single-component bilayers, three different system sizes + name: Simulations of different single-component bilayers, three different system + sizes publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/58d/654/58d654af9894439448a86b0c7a9f13020d41d54d/afaaae028c976185c3ce34198181af80a226d37f/README.yaml b/Simulations/58d/654/58d654af9894439448a86b0c7a9f13020d41d54d/afaaae028c976185c3ce34198181af80a226d37f/README.yaml index 5f2ffc1ab8..35bc5b489b 100644 --- a/Simulations/58d/654/58d654af9894439448a86b0c7a9f13020d41d54d/afaaae028c976185c3ce34198181af80a226d37f/README.yaml +++ b/Simulations/58d/654/58d654af9894439448a86b0c7a9f13020d41d54d/afaaae028c976185c3ce34198181af80a226d37f/README.yaml @@ -41,9 +41,12 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/1 AUTHORS_CONTACT: Hoelfich, Jullianne bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 300 K (FF-development, GROMACS, 500 ns) [NMRlipids simulation 835] + name: Molecular dynamics trajectory of a POPC bilayer at 300 K (FF-development, + GROMACS, 500 ns) [NMRlipids simulation 835] alternateName: POPCandTIP3P - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 300 K. Simulated with FF-development in GROMACS for 500 ns (32512 atoms). Deposited as NMRlipids Databank simulation 835 and available from https://doi.org/10.5281/zenodo.15328669. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 300 K. Simulated with FF-development in GROMACS for 500 ns (32512 atoms). Deposited + as NMRlipids Databank simulation 835 and available from https://doi.org/10.5281/zenodo.15328669. sameAs: https://doi.org/10.5281/zenodo.15328669 datePublished: '2025-05-02' license: diff --git a/Simulations/590/b36/590b3659e28c7cb041a14b5abab421196c4bbabd/05c2c0cd2052b2eb38080ab4b2d8205c6e13a4d1/README.yaml b/Simulations/590/b36/590b3659e28c7cb041a14b5abab421196c4bbabd/05c2c0cd2052b2eb38080ab4b2d8205c6e13a4d1/README.yaml index 0cd481d1b0..27032ef09c 100644 --- a/Simulations/590/b36/590b3659e28c7cb041a14b5abab421196c4bbabd/05c2c0cd2052b2eb38080ab4b2d8205c6e13a4d1/README.yaml +++ b/Simulations/590/b36/590b3659e28c7cb041a14b5abab421196c4bbabd/05c2c0cd2052b2eb38080ab4b2d8205c6e13a4d1/README.yaml @@ -63,9 +63,16 @@ EXPERIMENT: FORMFACTOR: [] ID: 411 bioschema_properties: - name: Molecular dynamics trajectory of a CLA/POPC/CAL/POPS/SOD (39:30:19:6:6) bilayer at 298 K (Lipid17 and Dang ions, GROMACS 2018.0, 950 ns) [NMRlipids simulation 411] + name: Molecular dynamics trajectory of a CLA/POPC/CAL/POPS/SOD (39:30:19:6:6) bilayer + at 298 K (Lipid17 and Dang ions, GROMACS 2018.0, 950 ns) [NMRlipids simulation + 411] alternateName: 60POPC_12POPS_3483SOL_12SOD_39CAL_78CLA_298K - description: Molecular dynamics trajectory of a lipid bilayer of 78 CLA (39 mol%), 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 30 mol%), 39 CAL (19 mol%), 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 6 mol%) and 12 SOD (6 mol%) at 298 K. Simulated with Lipid17 and Dang ions in GROMACS 2018.0 for 950 ns (20142 atoms). Deposited as NMRlipids Databank simulation 411 and available from https://doi.org/10.5281/zenodo.1487761. + description: Molecular dynamics trajectory of a lipid bilayer of 78 CLA (39 mol%), + 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 30 mol%), 39 CAL (19 + mol%), 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 6 mol%) and + 12 SOD (6 mol%) at 298 K. Simulated with Lipid17 and Dang ions in GROMACS 2018.0 + for 950 ns (20142 atoms). Deposited as NMRlipids Databank simulation 411 and available + from https://doi.org/10.5281/zenodo.1487761. sameAs: https://doi.org/10.5281/zenodo.1487761 datePublished: '2018-11-14' license: @@ -158,7 +165,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1487761 identifier: 10.5281/zenodo.1487761 url: https://doi.org/10.5281/zenodo.1487761 - name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS with the lipid17 force field, only counterions, and CaCl2 concentrations + name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS + with the lipid17 force field, only counterions, and CaCl2 concentrations publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/597/a0b/597a0b005b7c84d2ded6136833b0387e664008dd/3a1e9017c8c5966d7aa10f0c845e39681da9ddfa/README.yaml b/Simulations/597/a0b/597a0b005b7c84d2ded6136833b0387e664008dd/3a1e9017c8c5966d7aa10f0c845e39681da9ddfa/README.yaml index 6e65d120f7..26ce1f2308 100644 --- a/Simulations/597/a0b/597a0b005b7c84d2ded6136833b0387e664008dd/3a1e9017c8c5966d7aa10f0c845e39681da9ddfa/README.yaml +++ b/Simulations/597/a0b/597a0b005b7c84d2ded6136833b0387e664008dd/3a1e9017c8c5966d7aa10f0c845e39681da9ddfa/README.yaml @@ -63,9 +63,16 @@ EXPERIMENT: FORMFACTOR: [] ID: 540 bioschema_properties: - name: Molecular dynamics trajectory of a CLA/POT/POPC/POPS/SOD (34:34:22:4:4) bilayer at 298 K (Lipid17 and Dang ions, GROMACS 2018.0, 1000 ns) [NMRlipids simulation 540] + name: Molecular dynamics trajectory of a CLA/POT/POPC/POPS/SOD (34:34:22:4:4) bilayer + at 298 K (Lipid17 and Dang ions, GROMACS 2018.0, 1000 ns) [NMRlipids simulation + 540] alternateName: 12POPS_60POPC_3377SOL_12SOD_92POT_92CLA_298K - description: Molecular dynamics trajectory of a lipid bilayer of 92 CLA (34 mol%), 92 POT (34 mol%), 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 22 mol%), 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 4 mol%) and 12 SOD (4 mol%) at 298 K. Simulated with Lipid17 and Dang ions in GROMACS 2018.0 for 1000 ns (19891 atoms). Deposited as NMRlipids Databank simulation 540 and available from https://doi.org/10.5281/zenodo.1487895. + description: Molecular dynamics trajectory of a lipid bilayer of 92 CLA (34 mol%), + 92 POT (34 mol%), 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 22 + mol%), 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 4 mol%) and + 12 SOD (4 mol%) at 298 K. Simulated with Lipid17 and Dang ions in GROMACS 2018.0 + for 1000 ns (19891 atoms). Deposited as NMRlipids Databank simulation 540 and + available from https://doi.org/10.5281/zenodo.1487895. sameAs: https://doi.org/10.5281/zenodo.1487895 datePublished: '2018-11-14' license: @@ -158,7 +165,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1487895 identifier: 10.5281/zenodo.1487895 url: https://doi.org/10.5281/zenodo.1487895 - name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS with the lipid17 force field, NaCl and KCl salt concentrations + name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS + with the lipid17 force field, NaCl and KCl salt concentrations publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/59c/6b6/59c6b619af46db405ffdfd3fde0e1c6bd1f2cd1a/26c1e800add3822cc2e9d6a720a4725939544dde/README.yaml b/Simulations/59c/6b6/59c6b619af46db405ffdfd3fde0e1c6bd1f2cd1a/26c1e800add3822cc2e9d6a720a4725939544dde/README.yaml index def91a225f..4bdbed961d 100644 --- a/Simulations/59c/6b6/59c6b619af46db405ffdfd3fde0e1c6bd1f2cd1a/26c1e800add3822cc2e9d6a720a4725939544dde/README.yaml +++ b/Simulations/59c/6b6/59c6b619af46db405ffdfd3fde0e1c6bd1f2cd1a/26c1e800add3822cc2e9d6a720a4725939544dde/README.yaml @@ -51,9 +51,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 412 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (71:29) bilayer at 298.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 412] + name: Molecular dynamics trajectory of a POPC/CHOL (71:29) bilayer at 298.15 K (CHARMM36, + GROMACS, 1001 ns) [NMRlipids simulation 412] alternateName: 1024POPC_416CHOL_72000SOL_298K - description: Molecular dynamics trajectory of a lipid bilayer of 1024 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 71 mol%) and 416 CHOL (cholesterol, 29 mol%) at 298.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (384000 atoms). Deposited as NMRlipids Databank simulation 412 and available from https://doi.org/10.5281/zenodo.5767451. + description: Molecular dynamics trajectory of a lipid bilayer of 1024 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 71 mol%) and 416 CHOL (cholesterol, 29 mol%) at 298.15 K. Simulated with CHARMM36 + in GROMACS for 1001 ns (384000 atoms). Deposited as NMRlipids Databank simulation + 412 and available from https://doi.org/10.5281/zenodo.5767451. sameAs: https://doi.org/10.5281/zenodo.5767451 datePublished: '2021-12-08' license: diff --git a/Simulations/59d/326/59d326173355cd657c2572e38be43f9d1ca5fd46/d9275b2dba4deb293a62ec628f40e66a5e10618c/README.yaml b/Simulations/59d/326/59d326173355cd657c2572e38be43f9d1ca5fd46/d9275b2dba4deb293a62ec628f40e66a5e10618c/README.yaml index a6859376e2..9965fc0194 100644 --- a/Simulations/59d/326/59d326173355cd657c2572e38be43f9d1ca5fd46/d9275b2dba4deb293a62ec628f40e66a5e10618c/README.yaml +++ b/Simulations/59d/326/59d326173355cd657c2572e38be43f9d1ca5fd46/d9275b2dba4deb293a62ec628f40e66a5e10618c/README.yaml @@ -63,9 +63,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 184 bioschema_properties: - name: Molecular dynamics trajectory of a CES/POPC/CLA/POPS (34:32:25:8) bilayer at 310 K (Berger, GROMACS 4.0.7, 50 ns) [NMRlipids simulation 184] + name: Molecular dynamics trajectory of a CES/POPC/CLA/POPS (34:32:25:8) bilayer + at 310 K (Berger, GROMACS 4.0.7, 50 ns) [NMRlipids simulation 184] alternateName: 102POPC_26POPS_4290SOL_106CES_80CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 106 CES (34 mol%), 102 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 32 mol%), 80 CLA (25 mol%) and 26 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 8 mol%) at 310 K. Simulated with Berger in GROMACS 4.0.7 for 50 ns (19790 atoms). Deposited as NMRlipids Databank simulation 184 and available from https://doi.org/10.5281/zenodo.838229. + description: Molecular dynamics trajectory of a lipid bilayer of 106 CES (34 mol%), + 102 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 32 mol%), 80 CLA (25 + mol%) and 26 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 8 mol%) + at 310 K. Simulated with Berger in GROMACS 4.0.7 for 50 ns (19790 atoms). Deposited + as NMRlipids Databank simulation 184 and available from https://doi.org/10.5281/zenodo.838229. sameAs: https://doi.org/10.5281/zenodo.838229 datePublished: '2017-08-02' license: @@ -158,7 +163,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.838229 identifier: 10.5281/zenodo.838229 url: https://doi.org/10.5281/zenodo.838229 - name: Md Simulation Trajectory Of A Popc/Pops (4:1) Bilayer With 1M Cscl, Berger Force Field For Lipids, Dang'S For Cs+ And Ffgmx For Cl- + name: Md Simulation Trajectory Of A Popc/Pops (4:1) Bilayer With 1M Cscl, Berger + Force Field For Lipids, Dang'S For Cs+ And Ffgmx For Cl- publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/59d/c55/59dc55fcf5bb8ab2be3d7d94cedb56b131ee208a/f6b9602dc58447932b55a2d33dc5d31cff02a229/README.yaml b/Simulations/59d/c55/59dc55fcf5bb8ab2be3d7d94cedb56b131ee208a/f6b9602dc58447932b55a2d33dc5d31cff02a229/README.yaml index aac05b3b3f..eeaa02e7f5 100644 --- a/Simulations/59d/c55/59dc55fcf5bb8ab2be3d7d94cedb56b131ee208a/f6b9602dc58447932b55a2d33dc5d31cff02a229/README.yaml +++ b/Simulations/59d/c55/59dc55fcf5bb8ab2be3d7d94cedb56b131ee208a/f6b9602dc58447932b55a2d33dc5d31cff02a229/README.yaml @@ -48,9 +48,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 183 bioschema_properties: - name: Molecular dynamics trajectory of a SDPE/DOG (91:9) bilayer at 310 K (Lipid17, GROMACS 18.6, 2100 ns) [NMRlipids simulation 183] + name: Molecular dynamics trajectory of a SDPE/DOG (91:9) bilayer at 310 K (Lipid17, + GROMACS 18.6, 2100 ns) [NMRlipids simulation 183] alternateName: 9.4%DOGinSDPEwithLipid17 - description: Molecular dynamics trajectory of a lipid bilayer of 116 SDPE (1-stearoyl-2-docosahexaenoyl-sn-glycero-3-phosphoethanolamine, 91 mol%) and 12 DOG (1,2-dioleoyl-sn-glycerol, 9 mol%) at 310 K. Simulated with Lipid17 in GROMACS 18.6 for 2100 ns (36020 atoms). Deposited as NMRlipids Databank simulation 183 and available from https://doi.org/10.5281/zenodo.6778161. + description: Molecular dynamics trajectory of a lipid bilayer of 116 SDPE (1-stearoyl-2-docosahexaenoyl-sn-glycero-3-phosphoethanolamine, + 91 mol%) and 12 DOG (1,2-dioleoyl-sn-glycerol, 9 mol%) at 310 K. Simulated with + Lipid17 in GROMACS 18.6 for 2100 ns (36020 atoms). Deposited as NMRlipids Databank + simulation 183 and available from https://doi.org/10.5281/zenodo.6778161. sameAs: https://doi.org/10.5281/zenodo.6778161 datePublished: '2022-06-29' license: diff --git a/Simulations/5a0/e98/5a0e98712d109f8a8b5ccf4ee1726dab43fa894e/7d4a130e6a93b6655a550b5d4ba46949619a8c3b/README.yaml b/Simulations/5a0/e98/5a0e98712d109f8a8b5ccf4ee1726dab43fa894e/7d4a130e6a93b6655a550b5d4ba46949619a8c3b/README.yaml index ec9dc41909..c62b66b883 100644 --- a/Simulations/5a0/e98/5a0e98712d109f8a8b5ccf4ee1726dab43fa894e/7d4a130e6a93b6655a550b5d4ba46949619a8c3b/README.yaml +++ b/Simulations/5a0/e98/5a0e98712d109f8a8b5ccf4ee1726dab43fa894e/7d4a130e6a93b6655a550b5d4ba46949619a8c3b/README.yaml @@ -51,9 +51,13 @@ EXPERIMENT: CHOL: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a DOPC/CHOL (62:38) bilayer at 333.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 652] + name: Molecular dynamics trajectory of a DOPC/CHOL (62:38) bilayer at 333.15 K (CHARMM36, + GROMACS, 1001 ns) [NMRlipids simulation 652] alternateName: 1024DOPC_640CHOL_83200SOL_333K - description: Molecular dynamics trajectory of a lipid bilayer of 1024 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, 62 mol%) and 640 CHOL (cholesterol, 38 mol%) at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (438272 atoms). Deposited as NMRlipids Databank simulation 652 and available from https://doi.org/10.5281/zenodo.6943929. + description: Molecular dynamics trajectory of a lipid bilayer of 1024 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, + 62 mol%) and 640 CHOL (cholesterol, 38 mol%) at 333.15 K. Simulated with CHARMM36 + in GROMACS for 1001 ns (438272 atoms). Deposited as NMRlipids Databank simulation + 652 and available from https://doi.org/10.5281/zenodo.6943929. sameAs: https://doi.org/10.5281/zenodo.6943929 datePublished: '2022-07-30' license: diff --git a/Simulations/5a4/277/5a427728e5bcc18a6f162a8d325df4a9e4115250/f0fe9b9284aa683f9a419d9173d320cfa31d34cb/README.yaml b/Simulations/5a4/277/5a427728e5bcc18a6f162a8d325df4a9e4115250/f0fe9b9284aa683f9a419d9173d320cfa31d34cb/README.yaml index 80173c06fb..54fe29ec16 100644 --- a/Simulations/5a4/277/5a427728e5bcc18a6f162a8d325df4a9e4115250/f0fe9b9284aa683f9a419d9173d320cfa31d34cb/README.yaml +++ b/Simulations/5a4/277/5a427728e5bcc18a6f162a8d325df4a9e4115250/f0fe9b9284aa683f9a419d9173d320cfa31d34cb/README.yaml @@ -39,9 +39,12 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/1 ID: 617 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 298 K (Slipids, GROMACS, 100 ns) [NMRlipids simulation 617] + name: Molecular dynamics trajectory of a POPC bilayer at 298 K (Slipids, GROMACS, + 100 ns) [NMRlipids simulation 617] alternateName: POPC_T298K - description: Molecular dynamics trajectory of a lipid bilayer of 512 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 298 K. Simulated with Slipids in GROMACS for 100 ns (140437 atoms). Deposited as NMRlipids Databank simulation 617 and available from https://doi.org/10.5281/zenodo.166034. + description: Molecular dynamics trajectory of a lipid bilayer of 512 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 298 K. Simulated with Slipids in GROMACS for 100 ns (140437 atoms). Deposited + as NMRlipids Databank simulation 617 and available from https://doi.org/10.5281/zenodo.166034. sameAs: https://doi.org/10.5281/zenodo.166034 datePublished: '2016-11-21' license: @@ -132,7 +135,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.166034 identifier: 10.5281/zenodo.166034 url: https://doi.org/10.5281/zenodo.166034 - name: 'Md Simulation Trajectory Of A Lipid Bilayer: Pure Popc In Water. Slipids, Gromacs 4.6.3. 2016.' + name: 'Md Simulation Trajectory Of A Lipid Bilayer: Pure Popc In Water. Slipids, + Gromacs 4.6.3. 2016.' publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/5b5/593/5b55930ae87dfb632f26c4c38a7a66080e7cbb7d/461d64647820187739173ba9094a030f7d5532c2/README.yaml b/Simulations/5b5/593/5b55930ae87dfb632f26c4c38a7a66080e7cbb7d/461d64647820187739173ba9094a030f7d5532c2/README.yaml index ffd81f84ab..13fc37520e 100644 --- a/Simulations/5b5/593/5b55930ae87dfb632f26c4c38a7a66080e7cbb7d/461d64647820187739173ba9094a030f7d5532c2/README.yaml +++ b/Simulations/5b5/593/5b55930ae87dfb632f26c4c38a7a66080e7cbb7d/461d64647820187739173ba9094a030f7d5532c2/README.yaml @@ -41,9 +41,12 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 35 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC bilayer at 308 K (CHARMM36, GROMACS 2016.4, 50 ns) [NMRlipids simulation 35] + name: Molecular dynamics trajectory of a DPPC bilayer at 308 K (CHARMM36, GROMACS + 2016.4, 50 ns) [NMRlipids simulation 35] alternateName: 212DPPC_29826SOL_308K - description: Molecular dynamics trajectory of a lipid bilayer of 212 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) at 308 K. Simulated with CHARMM36 in GROMACS 2016.4 for 50 ns (117038 atoms). Deposited as NMRlipids Databank simulation 35 and available from https://doi.org/10.5281/zenodo.3950029. + description: Molecular dynamics trajectory of a lipid bilayer of 212 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) + at 308 K. Simulated with CHARMM36 in GROMACS 2016.4 for 50 ns (117038 atoms). + Deposited as NMRlipids Databank simulation 35 and available from https://doi.org/10.5281/zenodo.3950029. sameAs: https://doi.org/10.5281/zenodo.3950029 datePublished: '2020-07-20' license: @@ -143,7 +146,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3950029 identifier: 10.5281/zenodo.3950029 url: https://doi.org/10.5281/zenodo.3950029 - name: 212 DPPC Molecules bilayer in pure Water, simulated at temperatures ranging from 288K to 358K + name: 212 DPPC Molecules bilayer in pure Water, simulated at temperatures ranging + from 288K to 358K publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/5be/243/5be243a1f314270adfc363ead2ed40d71cc768cd/2495856d8abe5e5348b708a6d762e8e2a6ad3a51/README.yaml b/Simulations/5be/243/5be243a1f314270adfc363ead2ed40d71cc768cd/2495856d8abe5e5348b708a6d762e8e2a6ad3a51/README.yaml index b3e914a9d0..8041e70613 100644 --- a/Simulations/5be/243/5be243a1f314270adfc363ead2ed40d71cc768cd/2495856d8abe5e5348b708a6d762e8e2a6ad3a51/README.yaml +++ b/Simulations/5be/243/5be243a1f314270adfc363ead2ed40d71cc768cd/2495856d8abe5e5348b708a6d762e8e2a6ad3a51/README.yaml @@ -55,9 +55,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 187 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (59:20:20) bilayer at 298 K (Berger delivered by Peter Tieleman, GROMACS 4.5, 51 ns) [NMRlipids simulation 187] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (59:20:20) bilayer at 298 + K (Berger delivered by Peter Tieleman, GROMACS 4.5, 51 ns) [NMRlipids simulation + 187] alternateName: 128POPC_44SOD_44CLA_7202SOL_298K_Berger - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 59 mol%), 44 CLA (20 mol%) and 44 SOD (20 mol%) at 298 K. Simulated with Berger delivered by Peter Tieleman in GROMACS 4.5 for 51 ns (28350 atoms). Deposited as NMRlipids Databank simulation 187 and available from https://doi.org/10.5281/zenodo.32144. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 59 mol%), 44 CLA (20 mol%) and 44 SOD (20 mol%) at 298 K. Simulated with Berger + delivered by Peter Tieleman in GROMACS 4.5 for 51 ns (28350 atoms). Deposited + as NMRlipids Databank simulation 187 and available from https://doi.org/10.5281/zenodo.32144. sameAs: https://doi.org/10.5281/zenodo.32144 datePublished: '2015-10-15' license: @@ -146,7 +151,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.32144 identifier: 10.5281/zenodo.32144 url: https://doi.org/10.5281/zenodo.32144 - name: Md Simulation Trajectory And Related Files For Popc Bilayer With 340Mm Nacl (Berger Model Delivered By Tieleman, Ffgmx Ions, Gromacs 4.5) + name: Md Simulation Trajectory And Related Files For Popc Bilayer With 340Mm Nacl + (Berger Model Delivered By Tieleman, Ffgmx Ions, Gromacs 4.5) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/5c5/233/5c5233716e75bd7727a4867e3fe84bfd40e867ec/aa513d05342e2b2f0cd95f80e96055cd64167d99/README.yaml b/Simulations/5c5/233/5c5233716e75bd7727a4867e3fe84bfd40e867ec/aa513d05342e2b2f0cd95f80e96055cd64167d99/README.yaml index 110d1e3da0..97b0f12671 100644 --- a/Simulations/5c5/233/5c5233716e75bd7727a4867e3fe84bfd40e867ec/aa513d05342e2b2f0cd95f80e96055cd64167d99/README.yaml +++ b/Simulations/5c5/233/5c5233716e75bd7727a4867e3fe84bfd40e867ec/aa513d05342e2b2f0cd95f80e96055cd64167d99/README.yaml @@ -49,9 +49,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 234 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (38:31:31) bilayer at 310 K (Slipids with ions by Smith & Dang, GROMACS 4.6, 200 ns) [NMRlipids simulation 234] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (38:31:31) bilayer at 310 + K (Slipids with ions by Smith & Dang, GROMACS 4.6, 200 ns) [NMRlipids simulation + 234] alternateName: 200POPC_9000SOL_162SOD_162CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 38 mol%), 162 CLA (31 mol%) and 162 SOD (31 mol%) at 310 K. Simulated with Slipids with ions by Smith & Dang in GROMACS 4.6 for 200 ns (54124 atoms). Deposited as NMRlipids Databank simulation 234 and available from https://doi.org/10.5281/zenodo.259341. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 38 mol%), 162 CLA (31 mol%) and 162 SOD (31 mol%) at 310 K. Simulated with Slipids + with ions by Smith & Dang in GROMACS 4.6 for 200 ns (54124 atoms). Deposited as + NMRlipids Databank simulation 234 and available from https://doi.org/10.5281/zenodo.259341. sameAs: https://doi.org/10.5281/zenodo.259341 datePublished: '2017-01-24' license: @@ -139,7 +144,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.259341 identifier: 10.5281/zenodo.259341 url: https://doi.org/10.5281/zenodo.259341 - name: Popc With Varying Amounts Of Cholesterol, 1 M Of Nacl. Slipids With Ions By Smith & Dang + name: Popc With Varying Amounts Of Cholesterol, 1 M Of Nacl. Slipids With Ions + By Smith & Dang publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/5cb/4a4/5cb4a4f40e6c195328f0d90b89793b0b8abb3256/411f0068bcfa42f1b222bf3b2ea2bcaacdf3e249/README.yaml b/Simulations/5cb/4a4/5cb4a4f40e6c195328f0d90b89793b0b8abb3256/411f0068bcfa42f1b222bf3b2ea2bcaacdf3e249/README.yaml index a4e36afb74..6a3e9a83a8 100644 --- a/Simulations/5cb/4a4/5cb4a4f40e6c195328f0d90b89793b0b8abb3256/411f0068bcfa42f1b222bf3b2ea2bcaacdf3e249/README.yaml +++ b/Simulations/5cb/4a4/5cb4a4f40e6c195328f0d90b89793b0b8abb3256/411f0068bcfa42f1b222bf3b2ea2bcaacdf3e249/README.yaml @@ -58,9 +58,14 @@ EXPERIMENT: SM16: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a POPC/SM16/CHOL (40:40:20) bilayer at 295 K (Slipids, GROMACS 5.1.4, 100 ns) [NMRlipids simulation 762] + name: Molecular dynamics trajectory of a POPC/SM16/CHOL (40:40:20) bilayer at 295 + K (Slipids, GROMACS 5.1.4, 100 ns) [NMRlipids simulation 762] alternateName: Ternary mixture of POPC/PSM/Chol (2:2:1) at 295 K Slipids - description: Molecular dynamics trajectory of a lipid bilayer of 408 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 40 mol%), 408 SM16 (N-palmitoyl-D-erythro-sphingosylphosphorylcholine, 40 mol%) and 208 CHOL (cholesterol, 20 mol%) at 295 K. Simulated with Slipids in GROMACS 5.1.4 for 100 ns (229400 atoms). Deposited as NMRlipids Databank simulation 762 and available from https://doi.org/10.5281/zenodo.8307369. + description: Molecular dynamics trajectory of a lipid bilayer of 408 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 40 mol%), 408 SM16 (N-palmitoyl-D-erythro-sphingosylphosphorylcholine, 40 mol%) + and 208 CHOL (cholesterol, 20 mol%) at 295 K. Simulated with Slipids in GROMACS + 5.1.4 for 100 ns (229400 atoms). Deposited as NMRlipids Databank simulation 762 + and available from https://doi.org/10.5281/zenodo.8307369. sameAs: https://doi.org/10.5281/zenodo.8307369 datePublished: '2023-09-03' license: @@ -150,7 +155,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.8307369 identifier: 10.5281/zenodo.8307369 url: https://doi.org/10.5281/zenodo.8307369 - name: 'MD simulation trajectory of Ternary mixture of POPC/PSM/Chol (2:2:1) at 295 K: Slipids, GROMACS 5.1.4.' + name: 'MD simulation trajectory of Ternary mixture of POPC/PSM/Chol (2:2:1) at + 295 K: Slipids, GROMACS 5.1.4.' publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/5d3/ea3/5d3ea34ae3507e1e3332ae8796a6e9de530fd8e0/88949910e27ce2d96c8bb232b2b7647236920e31/README.yaml b/Simulations/5d3/ea3/5d3ea34ae3507e1e3332ae8796a6e9de530fd8e0/88949910e27ce2d96c8bb232b2b7647236920e31/README.yaml index 1dcb62ea83..b54f5be090 100644 --- a/Simulations/5d3/ea3/5d3ea34ae3507e1e3332ae8796a6e9de530fd8e0/88949910e27ce2d96c8bb232b2b7647236920e31/README.yaml +++ b/Simulations/5d3/ea3/5d3ea34ae3507e1e3332ae8796a6e9de530fd8e0/88949910e27ce2d96c8bb232b2b7647236920e31/README.yaml @@ -41,9 +41,12 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 310 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 303 K (CHARMM36, GROMACS 5.0.6, 500 ns) [NMRlipids simulation 310] + name: Molecular dynamics trajectory of a POPC bilayer at 303 K (CHARMM36, GROMACS + 5.0.6, 500 ns) [NMRlipids simulation 310] alternateName: 128POPC_4040SOL_10A-switch_v2 - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 303 K. Simulated with CHARMM36 in GROMACS 5.0.6 for 500 ns (29272 atoms). Deposited as NMRlipids Databank simulation 310 and available from https://doi.org/10.5281/zenodo.164203. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 303 K. Simulated with CHARMM36 in GROMACS 5.0.6 for 500 ns (29272 atoms). Deposited + as NMRlipids Databank simulation 310 and available from https://doi.org/10.5281/zenodo.164203. sameAs: https://doi.org/10.5281/zenodo.164203 datePublished: '2016-11-01' license: diff --git a/Simulations/5d8/e1e/5d8e1e55ac01defbd4e0ba53fcdaa2487aa6e6a7/34cd489a7e7c5b433e969a02c671a238b81ca2d4/README.yaml b/Simulations/5d8/e1e/5d8e1e55ac01defbd4e0ba53fcdaa2487aa6e6a7/34cd489a7e7c5b433e969a02c671a238b81ca2d4/README.yaml index 98144e258f..63721b2201 100644 --- a/Simulations/5d8/e1e/5d8e1e55ac01defbd4e0ba53fcdaa2487aa6e6a7/34cd489a7e7c5b433e969a02c671a238b81ca2d4/README.yaml +++ b/Simulations/5d8/e1e/5d8e1e55ac01defbd4e0ba53fcdaa2487aa6e6a7/34cd489a7e7c5b433e969a02c671a238b81ca2d4/README.yaml @@ -55,9 +55,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 174 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/POT (37:32:32) bilayer at 313 K (ECC-lipids, GROMACS 5.1.4, 300 ns) [NMRlipids simulation 174] + name: Molecular dynamics trajectory of a POPC/CLA/POT (37:32:32) bilayer at 313 + K (ECC-lipids, GROMACS 5.1.4, 300 ns) [NMRlipids simulation 174] alternateName: 128POPC_6232SOL_110POT_110CLA_313K - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 37 mol%), 110 CLA (32 mol%) and 110 POT (32 mol%) at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 300 ns (36068 atoms). Deposited as NMRlipids Databank simulation 174 and available from https://doi.org/10.5281/zenodo.3335503. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 37 mol%), 110 CLA (32 mol%) and 110 POT (32 mol%) at 313 K. Simulated with ECC-lipids + in GROMACS 5.1.4 for 300 ns (36068 atoms). Deposited as NMRlipids Databank simulation + 174 and available from https://doi.org/10.5281/zenodo.3335503. sameAs: https://doi.org/10.5281/zenodo.3335503 datePublished: '2017-12-19' license: @@ -149,7 +153,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3335503 identifier: 10.5281/zenodo.3335503 url: https://doi.org/10.5281/zenodo.3335503 - name: Simulations of POPC lipid bilayer in water solution at various NaCl, KCl and CaCl2 concentrations using ECC-POPC force field + name: Simulations of POPC lipid bilayer in water solution at various NaCl, KCl + and CaCl2 concentrations using ECC-POPC force field publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/5da/8ab/5da8aba490e2e91b6dfe33e5eb66d2a8fbb8b331/c064d9ff20e108fa13e1b83190ac62382bebb558/README.yaml b/Simulations/5da/8ab/5da8aba490e2e91b6dfe33e5eb66d2a8fbb8b331/c064d9ff20e108fa13e1b83190ac62382bebb558/README.yaml index 5cc325968a..75746e001a 100644 --- a/Simulations/5da/8ab/5da8aba490e2e91b6dfe33e5eb66d2a8fbb8b331/c064d9ff20e108fa13e1b83190ac62382bebb558/README.yaml +++ b/Simulations/5da/8ab/5da8aba490e2e91b6dfe33e5eb66d2a8fbb8b331/c064d9ff20e108fa13e1b83190ac62382bebb558/README.yaml @@ -67,9 +67,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 337 bioschema_properties: - name: Molecular dynamics trajectory of a CLA/POT/POPC/POPS/SOD (34:34:22:4:4) bilayer at 298 K (ECC-lipids, GROMACS 2018.0, 1000 ns) [NMRlipids simulation 337] + name: Molecular dynamics trajectory of a CLA/POT/POPC/POPS/SOD (34:34:22:4:4) bilayer + at 298 K (ECC-lipids, GROMACS 2018.0, 1000 ns) [NMRlipids simulation 337] alternateName: 12POPS_60POPC_3377SOL_12SOD_92POT_92CLA_298K - description: Molecular dynamics trajectory of a lipid bilayer of 92 CLA (34 mol%), 92 POT (34 mol%), 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 22 mol%), 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 4 mol%) and 12 SOD (4 mol%) at 298 K. Simulated with ECC-lipids in GROMACS 2018.0 for 1000 ns (19891 atoms). Deposited as NMRlipids Databank simulation 337 and available from https://doi.org/10.5281/zenodo.3332778. + description: Molecular dynamics trajectory of a lipid bilayer of 92 CLA (34 mol%), + 92 POT (34 mol%), 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 22 + mol%), 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 4 mol%) and + 12 SOD (4 mol%) at 298 K. Simulated with ECC-lipids in GROMACS 2018.0 for 1000 + ns (19891 atoms). Deposited as NMRlipids Databank simulation 337 and available + from https://doi.org/10.5281/zenodo.3332778. sameAs: https://doi.org/10.5281/zenodo.3332778 datePublished: '2018-11-14' license: @@ -162,7 +168,9 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3332778 identifier: 10.5281/zenodo.3332778 url: https://doi.org/10.5281/zenodo.3332778 - name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS (5:1) with ECC-lipids force field, and Na+ (K+) counterions at various additional concentrations of NaCl and KCl + name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS + (5:1) with ECC-lipids force field, and Na+ (K+) counterions at various additional + concentrations of NaCl and KCl publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/5df/4a1/5df4a17305f7f96be761e8e819cf0f851b952160/5df4a17305f7f96be761e8e819cf0f851b952160/README.yaml b/Simulations/5df/4a1/5df4a17305f7f96be761e8e819cf0f851b952160/5df4a17305f7f96be761e8e819cf0f851b952160/README.yaml index efea2bc1a4..8935cb8b87 100644 --- a/Simulations/5df/4a1/5df4a17305f7f96be761e8e819cf0f851b952160/5df4a17305f7f96be761e8e819cf0f851b952160/README.yaml +++ b/Simulations/5df/4a1/5df4a17305f7f96be761e8e819cf0f851b952160/5df4a17305f7f96be761e8e819cf0f851b952160/README.yaml @@ -39,9 +39,12 @@ EXPERIMENT: FORMFACTOR: - 10.1016/j.chemphyslip.2020.104892/2 bioschema_properties: - name: Molecular dynamics trajectory of a SDPC bilayer at 303.15 K (CHARMM36m, NAMD 3, 500 ns) [NMRlipids simulation 900] + name: Molecular dynamics trajectory of a SDPC bilayer at 303.15 K (CHARMM36m, NAMD + 3, 500 ns) [NMRlipids simulation 900] alternateName: SDPC(18:0(d35)/22:6) - description: Molecular dynamics trajectory of a lipid bilayer of 200 SDPC (1-stearoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine) at 303.15 K. Simulated with CHARMM36m in NAMD 3 for 500 ns (57200 atoms). Deposited as NMRlipids Databank simulation 900 and available from https://doi.org/10.5281/zenodo.18469822. + description: Molecular dynamics trajectory of a lipid bilayer of 200 SDPC (1-stearoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine) + at 303.15 K. Simulated with CHARMM36m in NAMD 3 for 500 ns (57200 atoms). Deposited + as NMRlipids Databank simulation 900 and available from https://doi.org/10.5281/zenodo.18469822. sameAs: https://doi.org/10.5281/zenodo.18469822 datePublished: '2026-02-03' license: @@ -133,7 +136,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.18469822 identifier: 10.5281/zenodo.18469822 url: https://doi.org/10.5281/zenodo.18469822 - name: 1-stearoyl(d35)-2-docosahexaenoyl-sn-glycero-3-phosphocholine (18:0(d35)/22:6n3PC) | SDPC lipid bilayer, 303K, CHARMM36m-WYF forcefield, NAMD 3.0.2, 2* 500 ns + name: 1-stearoyl(d35)-2-docosahexaenoyl-sn-glycero-3-phosphocholine (18:0(d35)/22:6n3PC) + | SDPC lipid bilayer, 303K, CHARMM36m-WYF forcefield, NAMD 3.0.2, 2* 500 ns publisher: Zenodo _source: api: datacite diff --git a/Simulations/5e0/76b/5e076b17c45fed32bf63492301f79167dda0cc8b/5e076b17c45fed32bf63492301f79167dda0cc8b/README.yaml b/Simulations/5e0/76b/5e076b17c45fed32bf63492301f79167dda0cc8b/5e076b17c45fed32bf63492301f79167dda0cc8b/README.yaml index 547be1da7d..47029348e7 100644 --- a/Simulations/5e0/76b/5e076b17c45fed32bf63492301f79167dda0cc8b/5e076b17c45fed32bf63492301f79167dda0cc8b/README.yaml +++ b/Simulations/5e0/76b/5e076b17c45fed32bf63492301f79167dda0cc8b/5e076b17c45fed32bf63492301f79167dda0cc8b/README.yaml @@ -54,9 +54,14 @@ EXPERIMENT: POPC: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a POPC/SM16/CLA/SOD (52:22:13:13) bilayer at 298 K (Charmm36, NAMD, 0 ns) [NMRlipids simulation 770] + name: Molecular dynamics trajectory of a POPC/SM16/CLA/SOD (52:22:13:13) bilayer + at 298 K (Charmm36, NAMD, 0 ns) [NMRlipids simulation 770] alternateName: POPC/PSM (70/30) NAMD - description: Molecular dynamics trajectory of a lipid bilayer of 140 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 52 mol%), 60 SM16 (N-palmitoyl-D-erythro-sphingosylphosphorylcholine, 22 mol%), 35 CLA (13 mol%) and 35 SOD (13 mol%) at 298 K. Simulated with Charmm36 in NAMD for 0 ns (68450 atoms). Deposited as NMRlipids Databank simulation 770 and available from https://doi.org/10.5281/zenodo.8357123. + description: Molecular dynamics trajectory of a lipid bilayer of 140 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 52 mol%), 60 SM16 (N-palmitoyl-D-erythro-sphingosylphosphorylcholine, 22 mol%), + 35 CLA (13 mol%) and 35 SOD (13 mol%) at 298 K. Simulated with Charmm36 in NAMD + for 0 ns (68450 atoms). Deposited as NMRlipids Databank simulation 770 and available + from https://doi.org/10.5281/zenodo.8357123. sameAs: https://doi.org/10.5281/zenodo.8357123 datePublished: '2023-09-18' license: diff --git a/Simulations/5e2/0fe/5e20fe22000d94eb54ce0e030c1dd2439796b331/839c970611cedad2e65068b6e412d84c12831ed6/README.yaml b/Simulations/5e2/0fe/5e20fe22000d94eb54ce0e030c1dd2439796b331/839c970611cedad2e65068b6e412d84c12831ed6/README.yaml index e1b7e3d197..1dcace5116 100644 --- a/Simulations/5e2/0fe/5e20fe22000d94eb54ce0e030c1dd2439796b331/839c970611cedad2e65068b6e412d84c12831ed6/README.yaml +++ b/Simulations/5e2/0fe/5e20fe22000d94eb54ce0e030c1dd2439796b331/839c970611cedad2e65068b6e412d84c12831ed6/README.yaml @@ -46,9 +46,14 @@ TRJ: - - traj.xtc ID: 146 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPG/SOD (33:33:33) bilayer at 298 K (lipid17ecc, GROMACS, 348 ns) [NMRlipids simulation 146] + name: Molecular dynamics trajectory of a POPC/POPG/SOD (33:33:33) bilayer at 298 + K (lipid17ecc, GROMACS, 348 ns) [NMRlipids simulation 146] alternateName: POPC:POPG(1:1)_T298K - description: Molecular dynamics trajectory of a lipid bilayer of 150 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 33 mol%), 150 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 33 mol%) and 150 SOD (33 mol%) at 298 K. Simulated with lipid17ecc in GROMACS for 348 ns (128895 atoms). Deposited as NMRlipids Databank simulation 146 and available from https://doi.org/10.5281/zenodo.3859339. + description: Molecular dynamics trajectory of a lipid bilayer of 150 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 33 mol%), 150 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 33 mol%) + and 150 SOD (33 mol%) at 298 K. Simulated with lipid17ecc in GROMACS for 348 ns + (128895 atoms). Deposited as NMRlipids Databank simulation 146 and available from + https://doi.org/10.5281/zenodo.3859339. sameAs: https://doi.org/10.5281/zenodo.3859339 datePublished: '2020-05-27' license: diff --git a/Simulations/5e2/b86/5e2b8657d07a24992b5149e5272f0d9ebd678707/509828760e99d6b6d59c7c280d168ce807649b3c/README.yaml b/Simulations/5e2/b86/5e2b8657d07a24992b5149e5272f0d9ebd678707/509828760e99d6b6d59c7c280d168ce807649b3c/README.yaml index 3788ac3bb3..d1503a3be1 100644 --- a/Simulations/5e2/b86/5e2b8657d07a24992b5149e5272f0d9ebd678707/509828760e99d6b6d59c7c280d168ce807649b3c/README.yaml +++ b/Simulations/5e2/b86/5e2b8657d07a24992b5149e5272f0d9ebd678707/509828760e99d6b6d59c7c280d168ce807649b3c/README.yaml @@ -44,9 +44,12 @@ EXPERIMENT: SOPC: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a SOPC bilayer at 333.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 631] + name: Molecular dynamics trajectory of a SOPC bilayer at 333.15 K (CHARMM36, GROMACS, + 1001 ns) [NMRlipids simulation 631] alternateName: 1024SOPC_51200SOL_333K - description: Molecular dynamics trajectory of a lipid bilayer of 1024 SOPC (1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (296960 atoms). Deposited as NMRlipids Databank simulation 631 and available from https://doi.org/10.5281/zenodo.6943413. + description: Molecular dynamics trajectory of a lipid bilayer of 1024 SOPC (1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (296960 atoms). Deposited + as NMRlipids Databank simulation 631 and available from https://doi.org/10.5281/zenodo.6943413. sameAs: https://doi.org/10.5281/zenodo.6943413 datePublished: '2022-07-30' license: @@ -134,7 +137,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.6943413 identifier: 10.5281/zenodo.6943413 url: https://doi.org/10.5281/zenodo.6943413 - name: Simulations of different single-component bilayers, three different system sizes + name: Simulations of different single-component bilayers, three different system + sizes publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/5e3/b2a/5e3b2ac952731e1e43d9c54db772bc717b6e64b3/b0ca668455035f858a2ea2f152c6790226cbb2fd/README.yaml b/Simulations/5e3/b2a/5e3b2ac952731e1e43d9c54db772bc717b6e64b3/b0ca668455035f858a2ea2f152c6790226cbb2fd/README.yaml index 79a63f8888..53f01b25ee 100644 --- a/Simulations/5e3/b2a/5e3b2ac952731e1e43d9c54db772bc717b6e64b3/b0ca668455035f858a2ea2f152c6790226cbb2fd/README.yaml +++ b/Simulations/5e3/b2a/5e3b2ac952731e1e43d9c54db772bc717b6e64b3/b0ca668455035f858a2ea2f152c6790226cbb2fd/README.yaml @@ -50,9 +50,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 406 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/CLA/SOD (82:9:9) bilayer at 305 K (Slipids, GROMACS, 500 ns) [NMRlipids simulation 406] + name: Molecular dynamics trajectory of a DPPC/CLA/SOD (82:9:9) bilayer at 305 K + (Slipids, GROMACS, 500 ns) [NMRlipids simulation 406] alternateName: 1152DPPC_46440SOL_124SOD_124CLA_305K - description: Molecular dynamics trajectory of a lipid bilayer of 1152 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 82 mol%), 124 CLA (9 mol%) and 124 SOD (9 mol%) at 305 K. Simulated with Slipids in GROMACS for 500 ns (289328 atoms). Deposited as NMRlipids Databank simulation 406 and available from https://doi.org/10.5281/zenodo.3539129. + description: Molecular dynamics trajectory of a lipid bilayer of 1152 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 82 mol%), 124 CLA (9 mol%) and 124 SOD (9 mol%) at 305 K. Simulated with Slipids + in GROMACS for 500 ns (289328 atoms). Deposited as NMRlipids Databank simulation + 406 and available from https://doi.org/10.5281/zenodo.3539129. sameAs: https://doi.org/10.5281/zenodo.3539129 datePublished: '2019-11-12' license: diff --git a/Simulations/5e7/2ac/5e72acc7ff399b442eb8b3c91674eba84b565717/5fec48dbe05fbba1839f411983a53629f1de4bd4/README.yaml b/Simulations/5e7/2ac/5e72acc7ff399b442eb8b3c91674eba84b565717/5fec48dbe05fbba1839f411983a53629f1de4bd4/README.yaml index 715cae9a67..e1461d4053 100644 --- a/Simulations/5e7/2ac/5e72acc7ff399b442eb8b3c91674eba84b565717/5fec48dbe05fbba1839f411983a53629f1de4bd4/README.yaml +++ b/Simulations/5e7/2ac/5e72acc7ff399b442eb8b3c91674eba84b565717/5fec48dbe05fbba1839f411983a53629f1de4bd4/README.yaml @@ -38,9 +38,12 @@ EXPERIMENT: FORMFACTOR: - 10.1016/j.bbamem.2011.07.022/9 bioschema_properties: - name: Molecular dynamics trajectory of a DLPC bilayer at 333 K (CHARMM36/LJ-PME, GROMACS Gromacs 2022, 100 ns) [NMRlipids simulation 919] + name: Molecular dynamics trajectory of a DLPC bilayer at 333 K (CHARMM36/LJ-PME, + GROMACS Gromacs 2022, 100 ns) [NMRlipids simulation 919] alternateName: Fully hydrated DLPC bilayer in SPC/E water (LJ-PME) - description: Molecular dynamics trajectory of a lipid bilayer of 100 DLPC (1,2-dilauroyl-sn-glycero-3-phosphocholine) at 333 K. Simulated with CHARMM36/LJ-PME in GROMACS Gromacs 2022 for 100 ns (23542 atoms). Deposited as NMRlipids Databank simulation 919 and available from https://doi.org/10.5281/zenodo.20579050. + description: Molecular dynamics trajectory of a lipid bilayer of 100 DLPC (1,2-dilauroyl-sn-glycero-3-phosphocholine) + at 333 K. Simulated with CHARMM36/LJ-PME in GROMACS Gromacs 2022 for 100 ns (23542 + atoms). Deposited as NMRlipids Databank simulation 919 and available from https://doi.org/10.5281/zenodo.20579050. sameAs: https://doi.org/10.5281/zenodo.20579050 datePublished: '2026-06-07' license: @@ -131,7 +134,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.20579050 identifier: 10.5281/zenodo.20579050 url: https://doi.org/10.5281/zenodo.20579050 - name: Fully hydrated DLPC bilayer at different temperatures simulated using CHARMM36 with LJ-PME and LJ-cutoff + name: Fully hydrated DLPC bilayer at different temperatures simulated using CHARMM36 + with LJ-PME and LJ-cutoff publisher: Zenodo _source: api: datacite diff --git a/Simulations/5f5/a7d/5f5a7de2397ac23ec9394001c118a71837f2fe57/d65f3b39967303df2c9df3f45cd3b591d9140b48/README.yaml b/Simulations/5f5/a7d/5f5a7de2397ac23ec9394001c118a71837f2fe57/d65f3b39967303df2c9df3f45cd3b591d9140b48/README.yaml index 7b50fa3553..685a2f7446 100644 --- a/Simulations/5f5/a7d/5f5a7de2397ac23ec9394001c118a71837f2fe57/d65f3b39967303df2c9df3f45cd3b591d9140b48/README.yaml +++ b/Simulations/5f5/a7d/5f5a7de2397ac23ec9394001c118a71837f2fe57/d65f3b39967303df2c9df3f45cd3b591d9140b48/README.yaml @@ -44,9 +44,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 598 bioschema_properties: - name: Molecular dynamics trajectory of a DOPC bilayer at 313.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 598] + name: Molecular dynamics trajectory of a DOPC bilayer at 313.15 K (CHARMM36, GROMACS, + 1001 ns) [NMRlipids simulation 598] alternateName: 256DOPC_12800SOL_313K - description: Molecular dynamics trajectory of a lipid bilayer of 256 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) at 313.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (73728 atoms). Deposited as NMRlipids Databank simulation 598 and available from https://doi.org/10.5281/zenodo.6943086. + description: Molecular dynamics trajectory of a lipid bilayer of 256 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) + at 313.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (73728 atoms). Deposited + as NMRlipids Databank simulation 598 and available from https://doi.org/10.5281/zenodo.6943086. sameAs: https://doi.org/10.5281/zenodo.6943086 datePublished: '2022-07-30' license: diff --git a/Simulations/5fc/43a/5fc43ad145381cb3771e74353a36856ff8e65d2f/a17d97babec638e6f00c218e2582afa04e6ae5d4/README.yaml b/Simulations/5fc/43a/5fc43ad145381cb3771e74353a36856ff8e65d2f/a17d97babec638e6f00c218e2582afa04e6ae5d4/README.yaml index e582fa6cac..1ff2fa1d6e 100644 --- a/Simulations/5fc/43a/5fc43ad145381cb3771e74353a36856ff8e65d2f/a17d97babec638e6f00c218e2582afa04e6ae5d4/README.yaml +++ b/Simulations/5fc/43a/5fc43ad145381cb3771e74353a36856ff8e65d2f/a17d97babec638e6f00c218e2582afa04e6ae5d4/README.yaml @@ -41,9 +41,12 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 433 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 303 K (CHARMM36, GROMACS 2020.1, 840 ns) [NMRlipids simulation 433] + name: Molecular dynamics trajectory of a POPC bilayer at 303 K (CHARMM36, GROMACS + 2020.1, 840 ns) [NMRlipids simulation 433] alternateName: 122POPC_4880SOL_303K - description: Molecular dynamics trajectory of a lipid bilayer of 122 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 303 K. Simulated with CHARMM36 in GROMACS 2020.1 for 840 ns (30988 atoms). Deposited as NMRlipids Databank simulation 433 and available from https://doi.org/10.5281/zenodo.4071264. + description: Molecular dynamics trajectory of a lipid bilayer of 122 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 303 K. Simulated with CHARMM36 in GROMACS 2020.1 for 840 ns (30988 atoms). + Deposited as NMRlipids Databank simulation 433 and available from https://doi.org/10.5281/zenodo.4071264. sameAs: https://doi.org/10.5281/zenodo.4071264 datePublished: '2020-10-07' license: @@ -133,7 +136,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.4071264 identifier: 10.5281/zenodo.4071264 url: https://doi.org/10.5281/zenodo.4071264 - name: CHARMM36 simulations of pure POPC bilayer and a bilayer containing 50% of cholesterol, T=303K + name: CHARMM36 simulations of pure POPC bilayer and a bilayer containing 50% of + cholesterol, T=303K publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/600/e7c/600e7c307d44161208b55c4108c75b7f488177c0/cd8ad0b9bbc8c2420b75d0fe980a1f6d6b3de4de/README.yaml b/Simulations/600/e7c/600e7c307d44161208b55c4108c75b7f488177c0/cd8ad0b9bbc8c2420b75d0fe980a1f6d6b3de4de/README.yaml index 30213ad6a4..f298932ac1 100644 --- a/Simulations/600/e7c/600e7c307d44161208b55c4108c75b7f488177c0/cd8ad0b9bbc8c2420b75d0fe980a1f6d6b3de4de/README.yaml +++ b/Simulations/600/e7c/600e7c307d44161208b55c4108c75b7f488177c0/cd8ad0b9bbc8c2420b75d0fe980a1f6d6b3de4de/README.yaml @@ -70,9 +70,15 @@ TRJ: SOFTWARE: gromacs ID: 3 bioschema_properties: - name: Molecular dynamics trajectory of a DMPC/SOD/SAPI/CLA/POPI/SLIPI (46:27:12:7:4:4) bilayer at 303.15 K (CHARMM36, GROMACS, 2000 ns) [NMRlipids simulation 3] + name: Molecular dynamics trajectory of a DMPC/SOD/SAPI/CLA/POPI/SLIPI (46:27:12:7:4:4) + bilayer at 303.15 K (CHARMM36, GROMACS, 2000 ns) [NMRlipids simulation 3] alternateName: DMPC/liverPI bilayer - description: Molecular dynamics trajectory of a lipid bilayer of 180 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine, 46 mol%), 104 SOD (27 mol%), 46 SAPI (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoinositol, 12 mol%), 28 CLA (7 mol%), 16 POPI (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoinositol, 4 mol%) and 14 SLIPI (1-stearoyl-2-linoleoyl-phosphatidylinositol(-1), 4 mol%) at 303.15 K. Simulated with CHARMM36 in GROMACS for 2000 ns (70516 atoms). Deposited as NMRlipids Databank simulation 3 and available from https://doi.org/10.5281/zenodo.4651415. + description: Molecular dynamics trajectory of a lipid bilayer of 180 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine, + 46 mol%), 104 SOD (27 mol%), 46 SAPI (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoinositol, + 12 mol%), 28 CLA (7 mol%), 16 POPI (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoinositol, + 4 mol%) and 14 SLIPI (1-stearoyl-2-linoleoyl-phosphatidylinositol(-1), 4 mol%) + at 303.15 K. Simulated with CHARMM36 in GROMACS for 2000 ns (70516 atoms). Deposited + as NMRlipids Databank simulation 3 and available from https://doi.org/10.5281/zenodo.4651415. sameAs: https://doi.org/10.5281/zenodo.4651415 datePublished: '2021-03-31' license: diff --git a/Simulations/604/eca/604eca7a89f7875f3edf9b2f944f64cdcedcee37/ddb1026383c836b4d961a8dafc4c640823e9ba38/README.yaml b/Simulations/604/eca/604eca7a89f7875f3edf9b2f944f64cdcedcee37/ddb1026383c836b4d961a8dafc4c640823e9ba38/README.yaml index 0a5d5f047e..410ce97b3b 100644 --- a/Simulations/604/eca/604eca7a89f7875f3edf9b2f944f64cdcedcee37/ddb1026383c836b4d961a8dafc4c640823e9ba38/README.yaml +++ b/Simulations/604/eca/604eca7a89f7875f3edf9b2f944f64cdcedcee37/ddb1026383c836b4d961a8dafc4c640823e9ba38/README.yaml @@ -45,9 +45,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 579 bioschema_properties: - name: Molecular dynamics trajectory of a POPE bilayer at 303 K (Berger-POPE-2004, GROMACS 4.0.7, 100 ns) [NMRlipids simulation 579] + name: Molecular dynamics trajectory of a POPE bilayer at 303 K (Berger-POPE-2004, + GROMACS 4.0.7, 100 ns) [NMRlipids simulation 579] alternateName: 128POPE_3552SOL_303K_v2 - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) at 303 K. Simulated with Berger-POPE-2004 in GROMACS 4.0.7 for 100 ns (17312 atoms). Deposited as NMRlipids Databank simulation 579 and available from https://doi.org/10.5281/zenodo.1293889. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) + at 303 K. Simulated with Berger-POPE-2004 in GROMACS 4.0.7 for 100 ns (17312 atoms). + Deposited as NMRlipids Databank simulation 579 and available from https://doi.org/10.5281/zenodo.1293889. sameAs: https://doi.org/10.5281/zenodo.1293889 datePublished: '2018-06-20' license: diff --git a/Simulations/607/7f4/6077f488f12ff9e4bb644957e84bcba0535d8d11/7a0227eef901a4fcfc27666938a5d4330bb0517b/README.yaml b/Simulations/607/7f4/6077f488f12ff9e4bb644957e84bcba0535d8d11/7a0227eef901a4fcfc27666938a5d4330bb0517b/README.yaml index ec4ad0de5f..cd1c0f04ed 100644 --- a/Simulations/607/7f4/6077f488f12ff9e4bb644957e84bcba0535d8d11/7a0227eef901a4fcfc27666938a5d4330bb0517b/README.yaml +++ b/Simulations/607/7f4/6077f488f12ff9e4bb644957e84bcba0535d8d11/7a0227eef901a4fcfc27666938a5d4330bb0517b/README.yaml @@ -52,9 +52,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 459 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (48:35:17) bilayer at 310.15 K (CHARMM36 noNBFIX, GROMACS, 897 ns) [NMRlipids simulation 459] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (48:35:17) bilayer at 310.15 + K (CHARMM36 noNBFIX, GROMACS, 897 ns) [NMRlipids simulation 459] alternateName: 200POPC_9000SOL_73CAL_146CLA_310K_noNBFIX - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 48 mol%), 146 CLA (35 mol%) and 73 CAL (17 mol%) at 310.15 K. Simulated with CHARMM36 noNBFIX in GROMACS for 897 ns (54019 atoms). Deposited as NMRlipids Databank simulation 459 and available from https://doi.org/10.5281/zenodo.3434396. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 48 mol%), 146 CLA (35 mol%) and 73 CAL (17 mol%) at 310.15 K. Simulated with CHARMM36 + noNBFIX in GROMACS for 897 ns (54019 atoms). Deposited as NMRlipids Databank simulation + 459 and available from https://doi.org/10.5281/zenodo.3434396. sameAs: https://doi.org/10.5281/zenodo.3434396 datePublished: '2019-09-17' license: diff --git a/Simulations/610/b6c/610b6c9d42359b77ad0f5b7faf597be20751b204/5f618260682019700eff0b4492b2a089ea72b20c/README.yaml b/Simulations/610/b6c/610b6c9d42359b77ad0f5b7faf597be20751b204/5f618260682019700eff0b4492b2a089ea72b20c/README.yaml index 5eb289910a..d5182d15f0 100644 --- a/Simulations/610/b6c/610b6c9d42359b77ad0f5b7faf597be20751b204/5f618260682019700eff0b4492b2a089ea72b20c/README.yaml +++ b/Simulations/610/b6c/610b6c9d42359b77ad0f5b7faf597be20751b204/5f618260682019700eff0b4492b2a089ea72b20c/README.yaml @@ -51,9 +51,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 388 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPS/SOD (71:14:14) bilayer at 298 K (CHARMM36, GROMACS, 100 ns) [NMRlipids simulation 388] + name: Molecular dynamics trajectory of a POPC/POPS/SOD (71:14:14) bilayer at 298 + K (CHARMM36, GROMACS, 100 ns) [NMRlipids simulation 388] alternateName: 110POPC_22POPS_22SOD_4620SOL_298K_v2 - description: Molecular dynamics trajectory of a lipid bilayer of 110 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 71 mol%), 22 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 14 mol%) and 22 SOD (14 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for 100 ns (31416 atoms). Deposited as NMRlipids Databank simulation 388 and available from https://doi.org/10.5281/zenodo.1182665. + description: Molecular dynamics trajectory of a lipid bilayer of 110 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 71 mol%), 22 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 14 mol%) + and 22 SOD (14 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for 100 ns (31416 + atoms). Deposited as NMRlipids Databank simulation 388 and available from https://doi.org/10.5281/zenodo.1182665. sameAs: https://doi.org/10.5281/zenodo.1182665 datePublished: '2018-02-21' license: @@ -141,7 +145,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1182665 identifier: 10.5281/zenodo.1182665 url: https://doi.org/10.5281/zenodo.1182665 - name: Charmm36 Pops/Popc Simulations (Versions 1 And 2) 298 K 1.0 Nm Lj Switching With Na Ions + name: Charmm36 Pops/Popc Simulations (Versions 1 And 2) 298 K 1.0 Nm Lj Switching + With Na Ions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/610/b7e/610b7e2bb70c37b03f76e9df5c35155e1c1fdcd8/70ef5dc839c5cf2c289da56ca897dbce46b4415f/README.yaml b/Simulations/610/b7e/610b7e2bb70c37b03f76e9df5c35155e1c1fdcd8/70ef5dc839c5cf2c289da56ca897dbce46b4415f/README.yaml index 3f430d87f4..601477b07e 100644 --- a/Simulations/610/b7e/610b7e2bb70c37b03f76e9df5c35155e1c1fdcd8/70ef5dc839c5cf2c289da56ca897dbce46b4415f/README.yaml +++ b/Simulations/610/b7e/610b7e2bb70c37b03f76e9df5c35155e1c1fdcd8/70ef5dc839c5cf2c289da56ca897dbce46b4415f/README.yaml @@ -53,9 +53,14 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 389 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPS/SOD (71:14:14) bilayer at 320 K (CHARMM36 with NBFIX, GROMACS 2018.6, 399 ns) [NMRlipids simulation 389] + name: Molecular dynamics trajectory of a POPC/POPS/SOD (71:14:14) bilayer at 320 + K (CHARMM36 with NBFIX, GROMACS 2018.6, 399 ns) [NMRlipids simulation 389] alternateName: 250POPC_50POPS_11207SOL_50SOD_320K - description: Molecular dynamics trajectory of a lipid bilayer of 250 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 71 mol%), 50 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 14 mol%) and 50 SOD (14 mol%) at 320 K. Simulated with CHARMM36 with NBFIX in GROMACS 2018.6 for 399 ns (73521 atoms). Deposited as NMRlipids Databank simulation 389 and available from https://doi.org/10.5281/zenodo.3371327. + description: Molecular dynamics trajectory of a lipid bilayer of 250 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 71 mol%), 50 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 14 mol%) + and 50 SOD (14 mol%) at 320 K. Simulated with CHARMM36 with NBFIX in GROMACS 2018.6 + for 399 ns (73521 atoms). Deposited as NMRlipids Databank simulation 389 and available + from https://doi.org/10.5281/zenodo.3371327. sameAs: https://doi.org/10.5281/zenodo.3371327 datePublished: '2019-08-19' license: diff --git a/Simulations/611/eb1/611eb1451b3406f9a07395e74c89a779da77dd0e/7dacf9299757643c2ab76db9536d80031346829f/README.yaml b/Simulations/611/eb1/611eb1451b3406f9a07395e74c89a779da77dd0e/7dacf9299757643c2ab76db9536d80031346829f/README.yaml index a5b64db633..2020eabda2 100644 --- a/Simulations/611/eb1/611eb1451b3406f9a07395e74c89a779da77dd0e/7dacf9299757643c2ab76db9536d80031346829f/README.yaml +++ b/Simulations/611/eb1/611eb1451b3406f9a07395e74c89a779da77dd0e/7dacf9299757643c2ab76db9536d80031346829f/README.yaml @@ -52,9 +52,13 @@ EXPERIMENT: - 10.1039/C4SM00066H/3 ID: 483 bioschema_properties: - name: Molecular dynamics trajectory of a POPS/SOD (50:50) bilayer at 298 K (Lipid17 and Dang ions, GROMACS 2018.0, 1000 ns) [NMRlipids simulation 483] + name: Molecular dynamics trajectory of a POPS/SOD (50:50) bilayer at 298 K (Lipid17 + and Dang ions, GROMACS 2018.0, 1000 ns) [NMRlipids simulation 483] alternateName: 72POPS_3600SOL_72SOD_298K - description: Molecular dynamics trajectory of a lipid bilayer of 72 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 50 mol%) and 72 SOD (50 mol%) at 298 K. Simulated with Lipid17 and Dang ions in GROMACS 2018.0 for 1000 ns (20016 atoms). Deposited as NMRlipids Databank simulation 483 and available from https://doi.org/10.5281/zenodo.1487761. + description: Molecular dynamics trajectory of a lipid bilayer of 72 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, + 50 mol%) and 72 SOD (50 mol%) at 298 K. Simulated with Lipid17 and Dang ions in + GROMACS 2018.0 for 1000 ns (20016 atoms). Deposited as NMRlipids Databank simulation + 483 and available from https://doi.org/10.5281/zenodo.1487761. sameAs: https://doi.org/10.5281/zenodo.1487761 datePublished: '2018-11-14' license: @@ -149,7 +153,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1487761 identifier: 10.5281/zenodo.1487761 url: https://doi.org/10.5281/zenodo.1487761 - name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS with the lipid17 force field, only counterions, and CaCl2 concentrations + name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS + with the lipid17 force field, only counterions, and CaCl2 concentrations publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/618/168/6181681b59d71d00209c1e86fbb17a78ec0888dc/4864b319f81a2778a8068d475ad2dbf9687c2d27/README.yaml b/Simulations/618/168/6181681b59d71d00209c1e86fbb17a78ec0888dc/4864b319f81a2778a8068d475ad2dbf9687c2d27/README.yaml index d337e11e26..5d5ca84f96 100644 --- a/Simulations/618/168/6181681b59d71d00209c1e86fbb17a78ec0888dc/4864b319f81a2778a8068d475ad2dbf9687c2d27/README.yaml +++ b/Simulations/618/168/6181681b59d71d00209c1e86fbb17a78ec0888dc/4864b319f81a2778a8068d475ad2dbf9687c2d27/README.yaml @@ -52,9 +52,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/5 ID: 525 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (80:20) bilayer at 298.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 525] + name: Molecular dynamics trajectory of a POPC/CHOL (80:20) bilayer at 298.15 K (CHARMM36, + GROMACS, 1001 ns) [NMRlipids simulation 525] alternateName: 64POPC_16CHOL_4000SOL_298K - description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 80 mol%) and 16 CHOL (cholesterol, 20 mol%) at 298.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (21760 atoms). Deposited as NMRlipids Databank simulation 525 and available from https://doi.org/10.5281/zenodo.5767451. + description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 80 mol%) and 16 CHOL (cholesterol, 20 mol%) at 298.15 K. Simulated with CHARMM36 + in GROMACS for 1001 ns (21760 atoms). Deposited as NMRlipids Databank simulation + 525 and available from https://doi.org/10.5281/zenodo.5767451. sameAs: https://doi.org/10.5281/zenodo.5767451 datePublished: '2021-12-08' license: diff --git a/Simulations/618/da6/618da67594715bf1d8f167ee207e672022bf1ef3/141e154e24515d5de05c75384088437896b19079/README.yaml b/Simulations/618/da6/618da67594715bf1d8f167ee207e672022bf1ef3/141e154e24515d5de05c75384088437896b19079/README.yaml index 645a8bd10e..5abc536c32 100644 --- a/Simulations/618/da6/618da67594715bf1d8f167ee207e672022bf1ef3/141e154e24515d5de05c75384088437896b19079/README.yaml +++ b/Simulations/618/da6/618da67594715bf1d8f167ee207e672022bf1ef3/141e154e24515d5de05c75384088437896b19079/README.yaml @@ -41,9 +41,12 @@ EXPERIMENT: FORMFACTOR: - 10.1021/acs.jctc.3c00648/1 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 300 K (FF-development, GROMACS, 500 ns) [NMRlipids simulation 836] + name: Molecular dynamics trajectory of a POPC bilayer at 300 K (FF-development, + GROMACS, 500 ns) [NMRlipids simulation 836] alternateName: POPCandTIP3P - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 300 K. Simulated with FF-development in GROMACS for 500 ns (32512 atoms). Deposited as NMRlipids Databank simulation 836 and available from https://doi.org/10.5281/zenodo.15065748. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 300 K. Simulated with FF-development in GROMACS for 500 ns (32512 atoms). Deposited + as NMRlipids Databank simulation 836 and available from https://doi.org/10.5281/zenodo.15065748. sameAs: https://doi.org/10.5281/zenodo.15065748 datePublished: '2025-03-21' license: diff --git a/Simulations/619/82f/61982f4b3b90dd668b854d65834693dbfeb7e6fa/cf97b0ce38155ddd3e3b345949d22f69ae948201/README.yaml b/Simulations/619/82f/61982f4b3b90dd668b854d65834693dbfeb7e6fa/cf97b0ce38155ddd3e3b345949d22f69ae948201/README.yaml index 77d61e1ba1..7377afe6ef 100644 --- a/Simulations/619/82f/61982f4b3b90dd668b854d65834693dbfeb7e6fa/cf97b0ce38155ddd3e3b345949d22f69ae948201/README.yaml +++ b/Simulations/619/82f/61982f4b3b90dd668b854d65834693dbfeb7e6fa/cf97b0ce38155ddd3e3b345949d22f69ae948201/README.yaml @@ -55,9 +55,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 326 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPS/SOD (71:14:14) bilayer at 298 K (Lipid17 and ff99 ions, GROMACS 2018.0, 425 ns) [NMRlipids simulation 326] + name: Molecular dynamics trajectory of a POPC/POPS/SOD (71:14:14) bilayer at 298 + K (Lipid17 and ff99 ions, GROMACS 2018.0, 425 ns) [NMRlipids simulation 326] alternateName: 12POPS_60POPC_3600SOL_12SOD_298K - description: Molecular dynamics trajectory of a lipid bilayer of 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 71 mol%), 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 14 mol%) and 12 SOD (14 mol%) at 298 K. Simulated with Lipid17 and ff99 ions in GROMACS 2018.0 for 425 ns (20376 atoms). Deposited as NMRlipids Databank simulation 326 and available from https://doi.org/10.5281/zenodo.1487906. + description: Molecular dynamics trajectory of a lipid bilayer of 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 71 mol%), 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 14 mol%) + and 12 SOD (14 mol%) at 298 K. Simulated with Lipid17 and ff99 ions in GROMACS + 2018.0 for 425 ns (20376 atoms). Deposited as NMRlipids Databank simulation 326 + and available from https://doi.org/10.5281/zenodo.1487906. sameAs: https://doi.org/10.5281/zenodo.1487906 datePublished: '2018-11-14' license: @@ -148,7 +153,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1487906 identifier: 10.5281/zenodo.1487906 url: https://doi.org/10.5281/zenodo.1487906 - name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS with the lipid17 force field and ff99 ions + name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS + with the lipid17 force field and ff99 ions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/620/e7e/620e7e473f437da500cb26f4283698b9979b9c3e/ca17d550c76a9365915b4f054efe441d839425ab/README.yaml b/Simulations/620/e7e/620e7e473f437da500cb26f4283698b9979b9c3e/ca17d550c76a9365915b4f054efe441d839425ab/README.yaml index 2f15ca82e0..d7439e88c1 100644 --- a/Simulations/620/e7e/620e7e473f437da500cb26f4283698b9979b9c3e/ca17d550c76a9365915b4f054efe441d839425ab/README.yaml +++ b/Simulations/620/e7e/620e7e473f437da500cb26f4283698b9979b9c3e/ca17d550c76a9365915b4f054efe441d839425ab/README.yaml @@ -55,9 +55,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 16 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (72:19:9) bilayer at 313 K (ECC-lipids, GROMACS 5.1.4, 300 ns) [NMRlipids simulation 16] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (72:19:9) bilayer at 313 K + (ECC-lipids, GROMACS 5.1.4, 300 ns) [NMRlipids simulation 16] alternateName: 128POPC_8978SOL_17CAL_34CLA_313K - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 72 mol%), 34 CLA (19 mol%) and 17 CAL (9 mol%) at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 300 ns (44137 atoms). Deposited as NMRlipids Databank simulation 16 and available from https://doi.org/10.5281/zenodo.3335503. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 72 mol%), 34 CLA (19 mol%) and 17 CAL (9 mol%) at 313 K. Simulated with ECC-lipids + in GROMACS 5.1.4 for 300 ns (44137 atoms). Deposited as NMRlipids Databank simulation + 16 and available from https://doi.org/10.5281/zenodo.3335503. sameAs: https://doi.org/10.5281/zenodo.3335503 datePublished: '2017-12-19' license: @@ -149,7 +153,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3335503 identifier: 10.5281/zenodo.3335503 url: https://doi.org/10.5281/zenodo.3335503 - name: Simulations of POPC lipid bilayer in water solution at various NaCl, KCl and CaCl2 concentrations using ECC-POPC force field + name: Simulations of POPC lipid bilayer in water solution at various NaCl, KCl + and CaCl2 concentrations using ECC-POPC force field publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/624/b8a/624b8ac53befe5084c69d2c7dae322bbd734852b/5ac5d5ed9780e9296c4715ea3d2d6bad800d63c2/README.yaml b/Simulations/624/b8a/624b8ac53befe5084c69d2c7dae322bbd734852b/5ac5d5ed9780e9296c4715ea3d2d6bad800d63c2/README.yaml index 556afa2979..915960944d 100644 --- a/Simulations/624/b8a/624b8ac53befe5084c69d2c7dae322bbd734852b/5ac5d5ed9780e9296c4715ea3d2d6bad800d63c2/README.yaml +++ b/Simulations/624/b8a/624b8ac53befe5084c69d2c7dae322bbd734852b/5ac5d5ed9780e9296c4715ea3d2d6bad800d63c2/README.yaml @@ -55,9 +55,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 410 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/CLA/SOD (41:29:29) bilayer at 323 K (Berger-DPPC-98, GROMACS 5.0.4, 120 ns) [NMRlipids simulation 410] + name: Molecular dynamics trajectory of a DPPC/CLA/SOD (41:29:29) bilayer at 323 + K (Berger-DPPC-98, GROMACS 5.0.4, 120 ns) [NMRlipids simulation 410] alternateName: 72DPPC_2778SOL_51SOD_51CLA_323K - description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 41 mol%), 51 CLA (29 mol%) and 51 SOD (29 mol%) at 323 K. Simulated with Berger-DPPC-98 in GROMACS 5.0.4 for 120 ns (12036 atoms). Deposited as NMRlipids Databank simulation 410 and available from https://doi.org/10.5281/zenodo.17210. + description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 41 mol%), 51 CLA (29 mol%) and 51 SOD (29 mol%) at 323 K. Simulated with Berger-DPPC-98 + in GROMACS 5.0.4 for 120 ns (12036 atoms). Deposited as NMRlipids Databank simulation + 410 and available from https://doi.org/10.5281/zenodo.17210. sameAs: https://doi.org/10.5281/zenodo.17210 datePublished: '2015-04-28' license: diff --git a/Simulations/627/f10/627f109a3f0966dd1ac26074c08e55dbf30dc1c3/90ae66b30e033c08b8f754a4a93053086913586e/DPPC_FragmentQuality.json b/Simulations/627/f10/627f109a3f0966dd1ac26074c08e55dbf30dc1c3/90ae66b30e033c08b8f754a4a93053086913586e/DPPC_FragmentQuality.json new file mode 100644 index 0000000000..db2c9004a4 --- /dev/null +++ b/Simulations/627/f10/627f109a3f0966dd1ac26074c08e55dbf30dc1c3/90ae66b30e033c08b8f754a4a93053086913586e/DPPC_FragmentQuality.json @@ -0,0 +1 @@ +{"sn-1": NaN, "sn-2": NaN, "headgroup": 0.6571, "total": 0.6571} \ No newline at end of file diff --git a/Simulations/627/f10/627f109a3f0966dd1ac26074c08e55dbf30dc1c3/90ae66b30e033c08b8f754a4a93053086913586e/DPPC_OrderParameters_quality.json b/Simulations/627/f10/627f109a3f0966dd1ac26074c08e55dbf30dc1c3/90ae66b30e033c08b8f754a4a93053086913586e/DPPC_OrderParameters_quality.json new file mode 100644 index 0000000000..e29adbc26c --- /dev/null +++ b/Simulations/627/f10/627f109a3f0966dd1ac26074c08e55dbf30dc1c3/90ae66b30e033c08b8f754a4a93053086913586e/DPPC_OrderParameters_quality.json @@ -0,0 +1,84 @@ +{ + "10.1021/bi00687a021/1": { + "M_G1C10_M M_G1C10H1_M": NaN, + "M_G1C10_M M_G1C10H2_M": NaN, + "M_G1C11_M M_G1C11H1_M": NaN, + "M_G1C11_M M_G1C11H2_M": NaN, + "M_G1C12_M M_G1C12H1_M": NaN, + "M_G1C12_M M_G1C12H2_M": NaN, + "M_G1C13_M M_G1C13H1_M": NaN, + "M_G1C13_M M_G1C13H2_M": NaN, + "M_G1C14_M M_G1C14H1_M": NaN, + "M_G1C14_M M_G1C14H2_M": NaN, + "M_G1C15_M M_G1C15H1_M": NaN, + "M_G1C15_M M_G1C15H2_M": NaN, + "M_G1C16_M M_G1C16H1_M": NaN, + "M_G1C16_M M_G1C16H2_M": NaN, + "M_G1C17_M M_G1C17H1_M": NaN, + "M_G1C17_M M_G1C17H2_M": NaN, + "M_G1C17_M M_G1C17H3_M": NaN, + "M_G1C3_M M_G1C3H1_M": NaN, + "M_G1C3_M M_G1C3H2_M": NaN, + "M_G1C4_M M_G1C4H1_M": NaN, + "M_G1C4_M M_G1C4H2_M": NaN, + "M_G1C5_M M_G1C5H1_M": NaN, + "M_G1C5_M M_G1C5H2_M": NaN, + "M_G1C6_M M_G1C6H1_M": NaN, + "M_G1C6_M M_G1C6H2_M": NaN, + "M_G1C7_M M_G1C7H1_M": NaN, + "M_G1C7_M M_G1C7H2_M": NaN, + "M_G1C8_M M_G1C8H1_M": NaN, + "M_G1C8_M M_G1C8H2_M": NaN, + "M_G1C9_M M_G1C9H1_M": NaN, + "M_G1C9_M M_G1C9H2_M": NaN, + "M_G1_M M_G1H1_M": NaN, + "M_G1_M M_G1H2_M": NaN, + "M_G2C10_M M_G2C10H1_M": NaN, + "M_G2C10_M M_G2C10H2_M": NaN, + "M_G2C11_M M_G2C11H1_M": NaN, + "M_G2C11_M M_G2C11H2_M": NaN, + "M_G2C12_M M_G2C12H1_M": NaN, + "M_G2C12_M M_G2C12H2_M": NaN, + "M_G2C13_M M_G2C13H1_M": NaN, + "M_G2C13_M M_G2C13H2_M": NaN, + "M_G2C14_M M_G2C14H1_M": NaN, + "M_G2C14_M M_G2C14H2_M": NaN, + "M_G2C15_M M_G2C15H1_M": NaN, + "M_G2C15_M M_G2C15H2_M": NaN, + "M_G2C16_M M_G2C16H1_M": NaN, + "M_G2C16_M M_G2C16H2_M": NaN, + "M_G2C17_M M_G2C17H1_M": NaN, + "M_G2C17_M M_G2C17H2_M": NaN, + "M_G2C17_M M_G2C17H3_M": NaN, + "M_G2C3_M M_G2C3H1_M": NaN, + "M_G2C3_M M_G2C3H2_M": NaN, + "M_G2C4_M M_G2C4H1_M": NaN, + "M_G2C4_M M_G2C4H2_M": NaN, + "M_G2C5_M M_G2C5H1_M": NaN, + "M_G2C5_M M_G2C5H2_M": NaN, + "M_G2C6_M M_G2C6H1_M": NaN, + "M_G2C6_M M_G2C6H2_M": NaN, + "M_G2C7_M M_G2C7H1_M": NaN, + "M_G2C7_M M_G2C7H2_M": NaN, + "M_G2C8_M M_G2C8H1_M": NaN, + "M_G2C8_M M_G2C8H2_M": NaN, + "M_G2C9_M M_G2C9H1_M": NaN, + "M_G2C9_M M_G2C9H2_M": NaN, + "M_G2_M M_G2H1_M": NaN, + "M_G3C4_M M_G3C4H1_M": 0.0304, + "M_G3C4_M M_G3C4H2_M": 0.0278, + "M_G3C5_M M_G3C5H1_M": 0.927, + "M_G3C5_M M_G3C5H2_M": 0.9145, + "M_G3N6C1_M M_G3N6C1H1_M": 0.9878, + "M_G3N6C1_M M_G3N6C1H2_M": 0.9872, + "M_G3N6C1_M M_G3N6C1H3_M": 0.9877, + "M_G3N6C2_M M_G3N6C2H1_M": 0.9879, + "M_G3N6C2_M M_G3N6C2H2_M": 0.9887, + "M_G3N6C2_M M_G3N6C2H3_M": 0.9883, + "M_G3N6C3_M M_G3N6C3H1_M": 0.9878, + "M_G3N6C3_M M_G3N6C3H2_M": 0.9878, + "M_G3N6C3_M M_G3N6C3H3_M": 0.9887, + "M_G3_M M_G3H1_M": 0.1171, + "M_G3_M M_G3H2_M": 0.9192 + } +} \ No newline at end of file diff --git a/Simulations/627/f10/627f109a3f0966dd1ac26074c08e55dbf30dc1c3/90ae66b30e033c08b8f754a4a93053086913586e/FormFactorQuality.json b/Simulations/627/f10/627f109a3f0966dd1ac26074c08e55dbf30dc1c3/90ae66b30e033c08b8f754a4a93053086913586e/FormFactorQuality.json new file mode 100644 index 0000000000..75509d3985 --- /dev/null +++ b/Simulations/627/f10/627f109a3f0966dd1ac26074c08e55dbf30dc1c3/90ae66b30e033c08b8f754a4a93053086913586e/FormFactorQuality.json @@ -0,0 +1 @@ +[0.1789, 83.3434] \ No newline at end of file diff --git a/Simulations/627/f10/627f109a3f0966dd1ac26074c08e55dbf30dc1c3/90ae66b30e033c08b8f754a4a93053086913586e/README.yaml b/Simulations/627/f10/627f109a3f0966dd1ac26074c08e55dbf30dc1c3/90ae66b30e033c08b8f754a4a93053086913586e/README.yaml index 09070abe47..95b1c7c465 100644 --- a/Simulations/627/f10/627f109a3f0966dd1ac26074c08e55dbf30dc1c3/90ae66b30e033c08b8f754a4a93053086913586e/README.yaml +++ b/Simulations/627/f10/627f109a3f0966dd1ac26074c08e55dbf30dc1c3/90ae66b30e033c08b8f754a4a93053086913586e/README.yaml @@ -39,3 +39,9 @@ NUMBER_OF_ATOMS: 53000 DATEOFRUNNING: 15/09/2026 TYPEOFSYSTEM: lipid bilayer ID: 934 +EXPERIMENT: + ORDERPARAMETER: + DPPC: + - 10.1021/bi00687a021/1 + FORMFACTOR: + - 10.1016/j.bbamem.2011.07.022/4 diff --git a/Simulations/627/f10/627f109a3f0966dd1ac26074c08e55dbf30dc1c3/90ae66b30e033c08b8f754a4a93053086913586e/SYSTEM_quality.json b/Simulations/627/f10/627f109a3f0966dd1ac26074c08e55dbf30dc1c3/90ae66b30e033c08b8f754a4a93053086913586e/SYSTEM_quality.json new file mode 100644 index 0000000000..53c6c61a5e --- /dev/null +++ b/Simulations/627/f10/627f109a3f0966dd1ac26074c08e55dbf30dc1c3/90ae66b30e033c08b8f754a4a93053086913586e/SYSTEM_quality.json @@ -0,0 +1 @@ +{"headgroup": 0.6571, "tails": 0.0, "total": 0.6571} \ No newline at end of file diff --git a/Simulations/629/152/6291525d811c9e55255d375ccd8e007f9ec196a5/3437b86309d76a4cc3ad59664b0a0bf80d594439/README.yaml b/Simulations/629/152/6291525d811c9e55255d375ccd8e007f9ec196a5/3437b86309d76a4cc3ad59664b0a0bf80d594439/README.yaml index 3447d92b2a..b3b606c029 100644 --- a/Simulations/629/152/6291525d811c9e55255d375ccd8e007f9ec196a5/3437b86309d76a4cc3ad59664b0a0bf80d594439/README.yaml +++ b/Simulations/629/152/6291525d811c9e55255d375ccd8e007f9ec196a5/3437b86309d76a4cc3ad59664b0a0bf80d594439/README.yaml @@ -55,9 +55,13 @@ EXPERIMENT: CHOL: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a POPE/CHOL/SDG (58:33:9) bilayer at 310 K (Lipid17, GROMACS 18.7, 1000 ns) [NMRlipids simulation 719] + name: Molecular dynamics trajectory of a POPE/CHOL/SDG (58:33:9) bilayer at 310 + K (Lipid17, GROMACS 18.7, 1000 ns) [NMRlipids simulation 719] alternateName: DOGandCHOLinSDPEwithLipid17 - description: Molecular dynamics trajectory of a lipid bilayer of 74 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 58 mol%), 42 CHOL (cholesterol, 33 mol%) and 12 SDG (1-stearoyl-2-docosahexaenoyl-sn-glycerol, 9 mol%) at 310 K. Simulated with Lipid17 in GROMACS 18.7 for 1000 ns (32998 atoms). Deposited as NMRlipids Databank simulation 719 and available from https://doi.org/10.5281/zenodo.6823087. + description: Molecular dynamics trajectory of a lipid bilayer of 74 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, + 58 mol%), 42 CHOL (cholesterol, 33 mol%) and 12 SDG (1-stearoyl-2-docosahexaenoyl-sn-glycerol, + 9 mol%) at 310 K. Simulated with Lipid17 in GROMACS 18.7 for 1000 ns (32998 atoms). + Deposited as NMRlipids Databank simulation 719 and available from https://doi.org/10.5281/zenodo.6823087. sameAs: https://doi.org/10.5281/zenodo.6823087 datePublished: '2022-07-12' license: diff --git a/Simulations/62b/65b/62b65b73414748e100d10baf7c47149717f2dba5/54c7c46c6861d6199df0118d71dcc08889c6b2b6/README.yaml b/Simulations/62b/65b/62b65b73414748e100d10baf7c47149717f2dba5/54c7c46c6861d6199df0118d71dcc08889c6b2b6/README.yaml index c1d36ad68f..5b4323a9ff 100644 --- a/Simulations/62b/65b/62b65b73414748e100d10baf7c47149717f2dba5/54c7c46c6861d6199df0118d71dcc08889c6b2b6/README.yaml +++ b/Simulations/62b/65b/62b65b73414748e100d10baf7c47149717f2dba5/54c7c46c6861d6199df0118d71dcc08889c6b2b6/README.yaml @@ -52,9 +52,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 155 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (88:8:4) bilayer at 310 K (CHARMM36 noNBFIX, GROMACS, 879 ns) [NMRlipids simulation 155] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (88:8:4) bilayer at 310 K + (CHARMM36 noNBFIX, GROMACS, 879 ns) [NMRlipids simulation 155] alternateName: 200POPC_9000SOL_9CAL_18CLA_310K_noNBFIX - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 88 mol%), 18 CLA (8 mol%) and 9 CAL (4 mol%) at 310 K. Simulated with CHARMM36 noNBFIX in GROMACS for 879 ns (53827 atoms). Deposited as NMRlipids Databank simulation 155 and available from https://doi.org/10.5281/zenodo.3434396. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 88 mol%), 18 CLA (8 mol%) and 9 CAL (4 mol%) at 310 K. Simulated with CHARMM36 + noNBFIX in GROMACS for 879 ns (53827 atoms). Deposited as NMRlipids Databank simulation + 155 and available from https://doi.org/10.5281/zenodo.3434396. sameAs: https://doi.org/10.5281/zenodo.3434396 datePublished: '2019-09-17' license: diff --git a/Simulations/634/7c3/6347c32827b3b569640b33fc36e8018f97b90b77/fe98149544e8a66e3f38672ac02bb37265106b60/README.yaml b/Simulations/634/7c3/6347c32827b3b569640b33fc36e8018f97b90b77/fe98149544e8a66e3f38672ac02bb37265106b60/README.yaml index e67cb7fdf7..f81dd302fb 100644 --- a/Simulations/634/7c3/6347c32827b3b569640b33fc36e8018f97b90b77/fe98149544e8a66e3f38672ac02bb37265106b60/README.yaml +++ b/Simulations/634/7c3/6347c32827b3b569640b33fc36e8018f97b90b77/fe98149544e8a66e3f38672ac02bb37265106b60/README.yaml @@ -48,9 +48,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 876 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (86:7:7) bilayer at 300 K (OPLS3e, GROMACS Desmond of Schrodinger 2019-4, 1000 ns) [NMRlipids simulation 876] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (86:7:7) bilayer at 300 K + (OPLS3e, GROMACS Desmond of Schrodinger 2019-4, 1000 ns) [NMRlipids simulation + 876] alternateName: POPC, 44 w/l, 300 K, 0.1 M NaCl - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 86 mol%), 16 CLA (7 mol%) and 16 SOD (7 mol%) at 300 K. Simulated with OPLS3e in GROMACS Desmond of Schrodinger 2019-4 for 1000 ns (53472 atoms). Deposited as NMRlipids Databank simulation 876 and available from https://doi.org/10.5281/zenodo.10203643. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 86 mol%), 16 CLA (7 mol%) and 16 SOD (7 mol%) at 300 K. Simulated with OPLS3e + in GROMACS Desmond of Schrodinger 2019-4 for 1000 ns (53472 atoms). Deposited + as NMRlipids Databank simulation 876 and available from https://doi.org/10.5281/zenodo.10203643. sameAs: https://doi.org/10.5281/zenodo.10203643 datePublished: '2022' license: @@ -141,7 +146,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.10203643 identifier: 10.5281/zenodo.10203643 url: https://doi.org/10.5281/zenodo.10203643 - name: MD simulation of POPC bilayer with OPLS3e force field, 100 mM NaCl part 1 + name: MD simulation of POPC bilayer with OPLS3e force field, 100 mM NaCl part + 1 publisher: Zenodo _source: api: datacite diff --git a/Simulations/63a/215/63a2158628d2c47aac330925d8b03b4a198407ee/6e1aef9b26dba4caff8ead7e2e691bc90fe97e68/README.yaml b/Simulations/63a/215/63a2158628d2c47aac330925d8b03b4a198407ee/6e1aef9b26dba4caff8ead7e2e691bc90fe97e68/README.yaml index 154e856efd..cfadf5148c 100644 --- a/Simulations/63a/215/63a2158628d2c47aac330925d8b03b4a198407ee/6e1aef9b26dba4caff8ead7e2e691bc90fe97e68/README.yaml +++ b/Simulations/63a/215/63a2158628d2c47aac330925d8b03b4a198407ee/6e1aef9b26dba4caff8ead7e2e691bc90fe97e68/README.yaml @@ -56,9 +56,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 456 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL/CLA/SOD (61:26:6:6) bilayer at 310.15 K (CHARMM36, GROMACS 5.0, 200 ns) [NMRlipids simulation 456] + name: Molecular dynamics trajectory of a POPC/CHOL/CLA/SOD (61:26:6:6) bilayer at + 310.15 K (CHARMM36, GROMACS 5.0, 200 ns) [NMRlipids simulation 456] alternateName: 86CHOL_200POPC_9000SOL_21SOD_21CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 61 mol%), 86 CHOL (cholesterol, 26 mol%), 21 CLA (6 mol%) and 21 SOD (6 mol%) at 310.15 K. Simulated with CHARMM36 in GROMACS 5.0 for 200 ns (60206 atoms). Deposited as NMRlipids Databank simulation 456 and available from https://doi.org/10.5281/zenodo.259392. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 61 mol%), 86 CHOL (cholesterol, 26 mol%), 21 CLA (6 mol%) and 21 SOD (6 mol%) + at 310.15 K. Simulated with CHARMM36 in GROMACS 5.0 for 200 ns (60206 atoms). + Deposited as NMRlipids Databank simulation 456 and available from https://doi.org/10.5281/zenodo.259392. sameAs: https://doi.org/10.5281/zenodo.259392 datePublished: '2017-01-24' license: @@ -148,7 +152,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.259392 identifier: 10.5281/zenodo.259392 url: https://doi.org/10.5281/zenodo.259392 - name: Popc With Varying Amounts Of Cholesterol, 130 Mm Of Nacl. Charmm36 With Default Charmm Ions + name: Popc With Varying Amounts Of Cholesterol, 130 Mm Of Nacl. Charmm36 With + Default Charmm Ions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/63a/479/63a47940524010d5a2ff46f0d4c89b4b69e0ad4f/9d9ca60b644e801ec759177e4b1cbe5bf413fe25/README.yaml b/Simulations/63a/479/63a47940524010d5a2ff46f0d4c89b4b69e0ad4f/9d9ca60b644e801ec759177e4b1cbe5bf413fe25/README.yaml index c292779697..b798c088ef 100644 --- a/Simulations/63a/479/63a47940524010d5a2ff46f0d4c89b4b69e0ad4f/9d9ca60b644e801ec759177e4b1cbe5bf413fe25/README.yaml +++ b/Simulations/63a/479/63a47940524010d5a2ff46f0d4c89b4b69e0ad4f/9d9ca60b644e801ec759177e4b1cbe5bf413fe25/README.yaml @@ -45,9 +45,12 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/1 ID: 457 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 300 K (MacRog, GROMACS, 500 ns) [NMRlipids simulation 457] + name: Molecular dynamics trajectory of a POPC bilayer at 300 K (MacRog, GROMACS, + 500 ns) [NMRlipids simulation 457] alternateName: 128POPC_5120SOL_300K - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 300 K. Simulated with MacRog in GROMACS for 500 ns (32512 atoms). Deposited as NMRlipids Databank simulation 457 and available from https://doi.org/10.5281/zenodo.3741793. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 300 K. Simulated with MacRog in GROMACS for 500 ns (32512 atoms). Deposited + as NMRlipids Databank simulation 457 and available from https://doi.org/10.5281/zenodo.3741793. sameAs: https://doi.org/10.5281/zenodo.3741793 datePublished: '2020-04-06' license: diff --git a/Simulations/63d/bae/63dbaef0fd321124376c8893e90c451e7805e90d/bd216e4bed36a9a06e2acea3075911701c14ade6/README.yaml b/Simulations/63d/bae/63dbaef0fd321124376c8893e90c451e7805e90d/bd216e4bed36a9a06e2acea3075911701c14ade6/README.yaml index 02614e0949..8ad00157f5 100644 --- a/Simulations/63d/bae/63dbaef0fd321124376c8893e90c451e7805e90d/bd216e4bed36a9a06e2acea3075911701c14ade6/README.yaml +++ b/Simulations/63d/bae/63dbaef0fd321124376c8893e90c451e7805e90d/bd216e4bed36a9a06e2acea3075911701c14ade6/README.yaml @@ -55,9 +55,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 209 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPS/SOD (71:14:14) bilayer at 298 K (ECC-lipids, SPC water model, ECC-ions, GROMACS 2018.0, 1544 ns) [NMRlipids simulation 209] + name: Molecular dynamics trajectory of a POPC/POPS/SOD (71:14:14) bilayer at 298 + K (ECC-lipids, SPC water model, ECC-ions, GROMACS 2018.0, 1544 ns) [NMRlipids + simulation 209] alternateName: 12POPS_60POPC_3600SOL_12SOD_298K_ECC-lipid - description: Molecular dynamics trajectory of a lipid bilayer of 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 71 mol%), 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 14 mol%) and 12 SOD (14 mol%) at 298 K. Simulated with ECC-lipids, SPC water model, ECC-ions in GROMACS 2018.0 for 1544 ns (20376 atoms). Deposited as NMRlipids Databank simulation 209 and available from https://doi.org/10.5281/zenodo.1488094. + description: Molecular dynamics trajectory of a lipid bilayer of 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 71 mol%), 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 14 mol%) + and 12 SOD (14 mol%) at 298 K. Simulated with ECC-lipids, SPC water model, ECC-ions + in GROMACS 2018.0 for 1544 ns (20376 atoms). Deposited as NMRlipids Databank simulation + 209 and available from https://doi.org/10.5281/zenodo.1488094. sameAs: https://doi.org/10.5281/zenodo.1488094 datePublished: '2018-11-14' license: @@ -148,7 +154,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1488094 identifier: 10.5281/zenodo.1488094 url: https://doi.org/10.5281/zenodo.1488094 - name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS (various mixtures) with ECC-lipids force field, and Na+ (K+) counterions + name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS + (various mixtures) with ECC-lipids force field, and Na+ (K+) counterions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/644/21f/64421fbc8aeb62548340c7ca21ac1394671989d7/09092816adf24c4a20d1598888312f7f794e31dd/README.yaml b/Simulations/644/21f/64421fbc8aeb62548340c7ca21ac1394671989d7/09092816adf24c4a20d1598888312f7f794e31dd/README.yaml index d408a4d63c..78b627f127 100644 --- a/Simulations/644/21f/64421fbc8aeb62548340c7ca21ac1394671989d7/09092816adf24c4a20d1598888312f7f794e31dd/README.yaml +++ b/Simulations/644/21f/64421fbc8aeb62548340c7ca21ac1394671989d7/09092816adf24c4a20d1598888312f7f794e31dd/README.yaml @@ -56,9 +56,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 214 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CHOL/CAL (40:29:17:14) bilayer at 310.15 K (CHARMM36, GROMACS 5.0, 2000 ns) [NMRlipids simulation 214] + name: Molecular dynamics trajectory of a POPC/CLA/CHOL/CAL (40:29:17:14) bilayer + at 310.15 K (CHARMM36, GROMACS 5.0, 2000 ns) [NMRlipids simulation 214] alternateName: 86CHOL_200POPC_9000SOL_73CAL_146CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 40 mol%), 146 CLA (29 mol%), 86 CHOL (cholesterol, 17 mol%) and 73 CAL (14 mol%) at 310.15 K. Simulated with CHARMM36 in GROMACS 5.0 for 2000 ns (60383 atoms). Deposited as NMRlipids Databank simulation 214 and available from https://doi.org/10.5281/zenodo.259365. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 40 mol%), 146 CLA (29 mol%), 86 CHOL (cholesterol, 17 mol%) and 73 CAL (14 mol%) + at 310.15 K. Simulated with CHARMM36 in GROMACS 5.0 for 2000 ns (60383 atoms). + Deposited as NMRlipids Databank simulation 214 and available from https://doi.org/10.5281/zenodo.259365. sameAs: https://doi.org/10.5281/zenodo.259365 datePublished: '2017-01-24' license: @@ -148,7 +152,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.259365 identifier: 10.5281/zenodo.259365 url: https://doi.org/10.5281/zenodo.259365 - name: Popc With Varying Amounts Of Cholesterol, 450 Mm Of Cacl_2. Charmm36 With Default Charmm Ions + name: Popc With Varying Amounts Of Cholesterol, 450 Mm Of Cacl_2. Charmm36 With + Default Charmm Ions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/64f/277/64f27772e410f8ae052ec6976cd430718ae476f6/667f6c5e4750b15b516a68c3a85dab4c6d2e03fd/README.yaml b/Simulations/64f/277/64f27772e410f8ae052ec6976cd430718ae476f6/667f6c5e4750b15b516a68c3a85dab4c6d2e03fd/README.yaml index 6288be0665..82209c71c5 100644 --- a/Simulations/64f/277/64f27772e410f8ae052ec6976cd430718ae476f6/667f6c5e4750b15b516a68c3a85dab4c6d2e03fd/README.yaml +++ b/Simulations/64f/277/64f27772e410f8ae052ec6976cd430718ae476f6/667f6c5e4750b15b516a68c3a85dab4c6d2e03fd/README.yaml @@ -51,9 +51,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 61 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/CLA/SOD (82:9:9) bilayer at 320 K (CHARMM36, GROMACS 5.0.4, 400 ns) [NMRlipids simulation 61] + name: Molecular dynamics trajectory of a DPPC/CLA/SOD (82:9:9) bilayer at 320 K + (CHARMM36, GROMACS 5.0.4, 400 ns) [NMRlipids simulation 61] alternateName: 512DPPC_20480SOL_55SOD_55CLA_320K - description: Molecular dynamics trajectory of a lipid bilayer of 512 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 82 mol%), 55 CLA (9 mol%) and 55 SOD (9 mol%) at 320 K. Simulated with CHARMM36 in GROMACS 5.0.4 for 400 ns (128110 atoms). Deposited as NMRlipids Databank simulation 61 and available from https://doi.org/10.5281/zenodo.16276. + description: Molecular dynamics trajectory of a lipid bilayer of 512 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 82 mol%), 55 CLA (9 mol%) and 55 SOD (9 mol%) at 320 K. Simulated with CHARMM36 + in GROMACS 5.0.4 for 400 ns (128110 atoms). Deposited as NMRlipids Databank simulation + 61 and available from https://doi.org/10.5281/zenodo.16276. sameAs: https://doi.org/10.5281/zenodo.16276 datePublished: '2015-03-23' license: diff --git a/Simulations/64f/277/64f27772e410f8ae052ec6976cd430718ae476f6/669d3598b0ccd13a3cbb1bf5f8e785fa8efaaa81/README.yaml b/Simulations/64f/277/64f27772e410f8ae052ec6976cd430718ae476f6/669d3598b0ccd13a3cbb1bf5f8e785fa8efaaa81/README.yaml index 9b0c86c16a..c135182ca1 100644 --- a/Simulations/64f/277/64f27772e410f8ae052ec6976cd430718ae476f6/669d3598b0ccd13a3cbb1bf5f8e785fa8efaaa81/README.yaml +++ b/Simulations/64f/277/64f27772e410f8ae052ec6976cd430718ae476f6/669d3598b0ccd13a3cbb1bf5f8e785fa8efaaa81/README.yaml @@ -50,9 +50,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 62 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/CLA/SOD (82:9:9) bilayer at 320 K (CHARMM36, GROMACS 5.0.4, 500 ns) [NMRlipids simulation 62] + name: Molecular dynamics trajectory of a DPPC/CLA/SOD (82:9:9) bilayer at 320 K + (CHARMM36, GROMACS 5.0.4, 500 ns) [NMRlipids simulation 62] alternateName: DPPC_512_NaCl_150mM_320K_v-rescale - description: Molecular dynamics trajectory of a lipid bilayer of 512 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 82 mol%), 55 CLA (9 mol%) and 55 SOD (9 mol%) at 320 K. Simulated with CHARMM36 in GROMACS 5.0.4 for 500 ns (128110 atoms). Deposited as NMRlipids Databank simulation 62 and available from https://doi.org/10.5281/zenodo.1009027. + description: Molecular dynamics trajectory of a lipid bilayer of 512 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 82 mol%), 55 CLA (9 mol%) and 55 SOD (9 mol%) at 320 K. Simulated with CHARMM36 + in GROMACS 5.0.4 for 500 ns (128110 atoms). Deposited as NMRlipids Databank simulation + 62 and available from https://doi.org/10.5281/zenodo.1009027. sameAs: https://doi.org/10.5281/zenodo.1009027 datePublished: '2017-10-11' license: diff --git a/Simulations/64f/f36/64ff367da9889f3eed56768300ea2f750cdceb2a/0c9cd0a8caaad237974c7d79b15bd4e92bf8df2d/README.yaml b/Simulations/64f/f36/64ff367da9889f3eed56768300ea2f750cdceb2a/0c9cd0a8caaad237974c7d79b15bd4e92bf8df2d/README.yaml index fa8ad27e77..bb86853b76 100644 --- a/Simulations/64f/f36/64ff367da9889f3eed56768300ea2f750cdceb2a/0c9cd0a8caaad237974c7d79b15bd4e92bf8df2d/README.yaml +++ b/Simulations/64f/f36/64ff367da9889f3eed56768300ea2f750cdceb2a/0c9cd0a8caaad237974c7d79b15bd4e92bf8df2d/README.yaml @@ -58,9 +58,13 @@ EXPERIMENT: TLCL_0H: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POT/CLA/TLCL_0H (71:17:8:5) bilayer at 303.15 K (CHARMM36, GROMACS 5.0.6, 500 ns) [NMRlipids simulation 777] + name: Molecular dynamics trajectory of a POPC/POT/CLA/TLCL_0H (71:17:8:5) bilayer + at 303.15 K (CHARMM36, GROMACS 5.0.6, 500 ns) [NMRlipids simulation 777] alternateName: TLCL:POPC(10%)50mM-CHARMM - description: Molecular dynamics trajectory of a lipid bilayer of 94 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 71 mol%), 22 POT (17 mol%), 10 CLA (8 mol%) and 6 TLCL_0H (tetralinoleoyl cardiolipin(2−), 5 mol%) at 303.15 K. Simulated with CHARMM36 in GROMACS 5.0.6 for 500 ns (46933 atoms). Deposited as NMRlipids Databank simulation 777 and available from https://doi.org/10.5281/zenodo.8383234. + description: Molecular dynamics trajectory of a lipid bilayer of 94 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 71 mol%), 22 POT (17 mol%), 10 CLA (8 mol%) and 6 TLCL_0H (tetralinoleoyl cardiolipin(2−), + 5 mol%) at 303.15 K. Simulated with CHARMM36 in GROMACS 5.0.6 for 500 ns (46933 + atoms). Deposited as NMRlipids Databank simulation 777 and available from https://doi.org/10.5281/zenodo.8383234. sameAs: https://doi.org/10.5281/zenodo.8383234 datePublished: '2023-09-27' license: diff --git a/Simulations/651/1b5/6511b51211884811d5720c39f94310ffd1206726/6c1a87d5bd2a587e0b8d4bf75fa272c17f200ce5/README.yaml b/Simulations/651/1b5/6511b51211884811d5720c39f94310ffd1206726/6c1a87d5bd2a587e0b8d4bf75fa272c17f200ce5/README.yaml index 8284746b5e..94a91badeb 100644 --- a/Simulations/651/1b5/6511b51211884811d5720c39f94310ffd1206726/6c1a87d5bd2a587e0b8d4bf75fa272c17f200ce5/README.yaml +++ b/Simulations/651/1b5/6511b51211884811d5720c39f94310ffd1206726/6c1a87d5bd2a587e0b8d4bf75fa272c17f200ce5/README.yaml @@ -55,9 +55,14 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 170 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/SOD/POPG/CLA (47:27:20:6) bilayer at 310 K (CHARMM36, GROMACS 5.1.2, 100 ns) [NMRlipids simulation 170] + name: Molecular dynamics trajectory of a POPC/SOD/POPG/CLA (47:27:20:6) bilayer + at 310 K (CHARMM36, GROMACS 5.1.2, 100 ns) [NMRlipids simulation 170] alternateName: 350POPC_150POPG_25000SOL_150SOD_310K_2 - description: Molecular dynamics trajectory of a lipid bilayer of 350 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 47 mol%), 198 SOD (27 mol%), 150 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 20 mol%) and 48 CLA (6 mol%) at 310 K. Simulated with CHARMM36 in GROMACS 5.1.2 for 100 ns (141196 atoms). Deposited as NMRlipids Databank simulation 170 and available from https://doi.org/10.5281/zenodo.2580902. + description: Molecular dynamics trajectory of a lipid bilayer of 350 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 47 mol%), 198 SOD (27 mol%), 150 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, + 20 mol%) and 48 CLA (6 mol%) at 310 K. Simulated with CHARMM36 in GROMACS 5.1.2 + for 100 ns (141196 atoms). Deposited as NMRlipids Databank simulation 170 and + available from https://doi.org/10.5281/zenodo.2580902. sameAs: https://doi.org/10.5281/zenodo.2580902 datePublished: '2019-03-01' license: @@ -150,7 +155,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.2580902 identifier: 10.5281/zenodo.2580902 url: https://doi.org/10.5281/zenodo.2580902 - name: CHARMM36 POPC-POPG 7:3 Bilayer Simulation (Last 100 ns, 150 mM NaCl, 310 K ) + name: CHARMM36 POPC-POPG 7:3 Bilayer Simulation (Last 100 ns, 150 mM NaCl, 310 + K ) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/657/ec5/657ec589ab054232ea119adfa859e9ea685248fd/3f83910c14748e23837449d33e97da2450ba16a5/README.yaml b/Simulations/657/ec5/657ec589ab054232ea119adfa859e9ea685248fd/3f83910c14748e23837449d33e97da2450ba16a5/README.yaml index 9cc8e3d3b0..3658660739 100644 --- a/Simulations/657/ec5/657ec589ab054232ea119adfa859e9ea685248fd/3f83910c14748e23837449d33e97da2450ba16a5/README.yaml +++ b/Simulations/657/ec5/657ec589ab054232ea119adfa859e9ea685248fd/3f83910c14748e23837449d33e97da2450ba16a5/README.yaml @@ -44,9 +44,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 349 bioschema_properties: - name: Molecular dynamics trajectory of a POPE bilayer at 313 K (GROMOS 43A1-S3, GROMACS 4.0.7, 100 ns) [NMRlipids simulation 349] + name: Molecular dynamics trajectory of a POPE bilayer at 313 K (GROMOS 43A1-S3, + GROMACS 4.0.7, 100 ns) [NMRlipids simulation 349] alternateName: 128POPE_3552SOL_313K_v2 - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) at 313 K. Simulated with GROMOS 43A1-S3 in GROMACS 4.0.7 for 100 ns (17312 atoms). Deposited as NMRlipids Databank simulation 349 and available from https://doi.org/10.5281/zenodo.1293762. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) + at 313 K. Simulated with GROMOS 43A1-S3 in GROMACS 4.0.7 for 100 ns (17312 atoms). + Deposited as NMRlipids Databank simulation 349 and available from https://doi.org/10.5281/zenodo.1293762. sameAs: https://doi.org/10.5281/zenodo.1293762 datePublished: '2018-06-20' license: @@ -132,7 +135,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1293762 identifier: 10.5281/zenodo.1293762 url: https://doi.org/10.5281/zenodo.1293762 - name: 'Gromos 43A1-S3 Pope Simulations (Versions 1 And 2) 313 K (Note: Anisotropic Pressure Coupling)' + name: 'Gromos 43A1-S3 Pope Simulations (Versions 1 And 2) 313 K (Note: Anisotropic + Pressure Coupling)' publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/65e/ad5/65ead5c30b3b5515fda964d9633efdc5f1c7564f/7f55a988ff127851d7b4845d80de222a96e1944f/README.yaml b/Simulations/65e/ad5/65ead5c30b3b5515fda964d9633efdc5f1c7564f/7f55a988ff127851d7b4845d80de222a96e1944f/README.yaml index 74ddcbfd2f..8600236911 100644 --- a/Simulations/65e/ad5/65ead5c30b3b5515fda964d9633efdc5f1c7564f/7f55a988ff127851d7b4845d80de222a96e1944f/README.yaml +++ b/Simulations/65e/ad5/65ead5c30b3b5515fda964d9633efdc5f1c7564f/7f55a988ff127851d7b4845d80de222a96e1944f/README.yaml @@ -52,9 +52,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 162 bioschema_properties: - name: Molecular dynamics trajectory of a CLA/POPC/CAL (48:28:24) bilayer at 313 K (ECC-lipids, GROMACS, 1292 ns) [NMRlipids simulation 162] + name: Molecular dynamics trajectory of a CLA/POPC/CAL (48:28:24) bilayer at 313 + K (ECC-lipids, GROMACS, 1292 ns) [NMRlipids simulation 162] alternateName: 512POPC_24928SOL_440CAL_880CLA_313K - description: Molecular dynamics trajectory of a lipid bilayer of 880 CLA (48 mol%), 512 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 28 mol%) and 440 CAL (24 mol%) at 313 K. Simulated with ECC-lipids in GROMACS for 1292 ns (144712 atoms). Deposited as NMRlipids Databank simulation 162 and available from https://doi.org/10.5281/zenodo.3434100. + description: Molecular dynamics trajectory of a lipid bilayer of 880 CLA (48 mol%), + 512 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 28 mol%) and 440 CAL + (24 mol%) at 313 K. Simulated with ECC-lipids in GROMACS for 1292 ns (144712 atoms). + Deposited as NMRlipids Databank simulation 162 and available from https://doi.org/10.5281/zenodo.3434100. sameAs: https://doi.org/10.5281/zenodo.3434100 datePublished: '2019-09-17' license: diff --git a/Simulations/66b/22e/66b22ee83575dcbca5a36163c773cc4d93534418/207dcbf19b201fbe39855937864886eae03e2dac/README.yaml b/Simulations/66b/22e/66b22ee83575dcbca5a36163c773cc4d93534418/207dcbf19b201fbe39855937864886eae03e2dac/README.yaml index 3459a86852..298692fc1d 100644 --- a/Simulations/66b/22e/66b22ee83575dcbca5a36163c773cc4d93534418/207dcbf19b201fbe39855937864886eae03e2dac/README.yaml +++ b/Simulations/66b/22e/66b22ee83575dcbca5a36163c773cc4d93534418/207dcbf19b201fbe39855937864886eae03e2dac/README.yaml @@ -51,9 +51,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 24 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/CLA/SOD (82:9:9) bilayer at 320 K (CHARMM36, GROMACS 5.0.4, 300 ns) [NMRlipids simulation 24] + name: Molecular dynamics trajectory of a DPPC/CLA/SOD (82:9:9) bilayer at 320 K + (CHARMM36, GROMACS 5.0.4, 300 ns) [NMRlipids simulation 24] alternateName: 512DPPC_20480SOL_55SOD_55CLA_320K - description: Molecular dynamics trajectory of a lipid bilayer of 512 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 82 mol%), 55 CLA (9 mol%) and 55 SOD (9 mol%) at 320 K. Simulated with CHARMM36 in GROMACS 5.0.4 for 300 ns (128110 atoms). Deposited as NMRlipids Databank simulation 24 and available from https://doi.org/10.5281/zenodo.16258. + description: Molecular dynamics trajectory of a lipid bilayer of 512 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 82 mol%), 55 CLA (9 mol%) and 55 SOD (9 mol%) at 320 K. Simulated with CHARMM36 + in GROMACS 5.0.4 for 300 ns (128110 atoms). Deposited as NMRlipids Databank simulation + 24 and available from https://doi.org/10.5281/zenodo.16258. sameAs: https://doi.org/10.5281/zenodo.16258 datePublished: '2015-03-21' license: diff --git a/Simulations/66b/22e/66b22ee83575dcbca5a36163c773cc4d93534418/5ec47279ff3405236a3f30385728163ad0286264/README.yaml b/Simulations/66b/22e/66b22ee83575dcbca5a36163c773cc4d93534418/5ec47279ff3405236a3f30385728163ad0286264/README.yaml index 0017545117..bb48e6a786 100644 --- a/Simulations/66b/22e/66b22ee83575dcbca5a36163c773cc4d93534418/5ec47279ff3405236a3f30385728163ad0286264/README.yaml +++ b/Simulations/66b/22e/66b22ee83575dcbca5a36163c773cc4d93534418/5ec47279ff3405236a3f30385728163ad0286264/README.yaml @@ -50,9 +50,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 23 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/CLA/SOD (82:9:9) bilayer at 320 K (CHARMM36, GROMACS 5.0.4, 700 ns) [NMRlipids simulation 23] + name: Molecular dynamics trajectory of a DPPC/CLA/SOD (82:9:9) bilayer at 320 K + (CHARMM36, GROMACS 5.0.4, 700 ns) [NMRlipids simulation 23] alternateName: DPPC_512_NaCl_150mM_320K - description: Molecular dynamics trajectory of a lipid bilayer of 512 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 82 mol%), 55 CLA (9 mol%) and 55 SOD (9 mol%) at 320 K. Simulated with CHARMM36 in GROMACS 5.0.4 for 700 ns (128110 atoms). Deposited as NMRlipids Databank simulation 23 and available from https://doi.org/10.5281/zenodo.1009027. + description: Molecular dynamics trajectory of a lipid bilayer of 512 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 82 mol%), 55 CLA (9 mol%) and 55 SOD (9 mol%) at 320 K. Simulated with CHARMM36 + in GROMACS 5.0.4 for 700 ns (128110 atoms). Deposited as NMRlipids Databank simulation + 23 and available from https://doi.org/10.5281/zenodo.1009027. sameAs: https://doi.org/10.5281/zenodo.1009027 datePublished: '2017-10-11' license: diff --git a/Simulations/66f/81c/66f81c7905a792bfdc935f463c56af8bb1a1e31f/7050b07cc869d03e5645bc7935a4989dc0480766/README.yaml b/Simulations/66f/81c/66f81c7905a792bfdc935f463c56af8bb1a1e31f/7050b07cc869d03e5645bc7935a4989dc0480766/README.yaml index aa69b79400..d522625c1b 100644 --- a/Simulations/66f/81c/66f81c7905a792bfdc935f463c56af8bb1a1e31f/7050b07cc869d03e5645bc7935a4989dc0480766/README.yaml +++ b/Simulations/66f/81c/66f81c7905a792bfdc935f463c56af8bb1a1e31f/7050b07cc869d03e5645bc7935a4989dc0480766/README.yaml @@ -55,9 +55,13 @@ TRJLENGTH: 200010.0 DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 272 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/DHMDMAB (53:23:23) bilayer at 313 K (CHARMM36, GROMACS, 200 ns) [NMRlipids simulation 272] + name: Molecular dynamics trajectory of a POPC/CLA/DHMDMAB (53:23:23) bilayer at + 313 K (CHARMM36, GROMACS, 200 ns) [NMRlipids simulation 272] alternateName: POPC10%DHMDMAB_T313K - description: Molecular dynamics trajectory of a lipid bilayer of 100 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 53 mol%), 44 CLA (23 mol%) and 44 DHMDMAB (dihexadecyldimethylammonium, 23 mol%) at 313 K. Simulated with CHARMM36 in GROMACS for 200 ns (42050 atoms). Deposited as NMRlipids Databank simulation 272 and available from https://doi.org/10.5281/zenodo.1288297. + description: Molecular dynamics trajectory of a lipid bilayer of 100 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 53 mol%), 44 CLA (23 mol%) and 44 DHMDMAB (dihexadecyldimethylammonium, 23 mol%) + at 313 K. Simulated with CHARMM36 in GROMACS for 200 ns (42050 atoms). Deposited + as NMRlipids Databank simulation 272 and available from https://doi.org/10.5281/zenodo.1288297. sameAs: https://doi.org/10.5281/zenodo.1288297 datePublished: '2018-06-13' license: diff --git a/Simulations/670/484/6704849a21596a96b4e490419f3c937d719b2904/718296d4c5b00da31a47037e847ab0d5c5246d2c/DPPC_FragmentQuality.json b/Simulations/670/484/6704849a21596a96b4e490419f3c937d719b2904/718296d4c5b00da31a47037e847ab0d5c5246d2c/DPPC_FragmentQuality.json new file mode 100644 index 0000000000..dc5205e894 --- /dev/null +++ b/Simulations/670/484/6704849a21596a96b4e490419f3c937d719b2904/718296d4c5b00da31a47037e847ab0d5c5246d2c/DPPC_FragmentQuality.json @@ -0,0 +1 @@ +{"sn-1": NaN, "sn-2": NaN, "headgroup": 0.6118, "total": 0.6118} \ No newline at end of file diff --git a/Simulations/670/484/6704849a21596a96b4e490419f3c937d719b2904/718296d4c5b00da31a47037e847ab0d5c5246d2c/DPPC_OrderParameters_quality.json b/Simulations/670/484/6704849a21596a96b4e490419f3c937d719b2904/718296d4c5b00da31a47037e847ab0d5c5246d2c/DPPC_OrderParameters_quality.json new file mode 100644 index 0000000000..de3c72b8b3 --- /dev/null +++ b/Simulations/670/484/6704849a21596a96b4e490419f3c937d719b2904/718296d4c5b00da31a47037e847ab0d5c5246d2c/DPPC_OrderParameters_quality.json @@ -0,0 +1,84 @@ +{ + "10.1021/bi00687a021/1": { + "M_G1C10_M M_G1C10H1_M": NaN, + "M_G1C10_M M_G1C10H2_M": NaN, + "M_G1C11_M M_G1C11H1_M": NaN, + "M_G1C11_M M_G1C11H2_M": NaN, + "M_G1C12_M M_G1C12H1_M": NaN, + "M_G1C12_M M_G1C12H2_M": NaN, + "M_G1C13_M M_G1C13H1_M": NaN, + "M_G1C13_M M_G1C13H2_M": NaN, + "M_G1C14_M M_G1C14H1_M": NaN, + "M_G1C14_M M_G1C14H2_M": NaN, + "M_G1C15_M M_G1C15H1_M": NaN, + "M_G1C15_M M_G1C15H2_M": NaN, + "M_G1C16_M M_G1C16H1_M": NaN, + "M_G1C16_M M_G1C16H2_M": NaN, + "M_G1C17_M M_G1C17H1_M": NaN, + "M_G1C17_M M_G1C17H2_M": NaN, + "M_G1C17_M M_G1C17H3_M": NaN, + "M_G1C3_M M_G1C3H1_M": NaN, + "M_G1C3_M M_G1C3H2_M": NaN, + "M_G1C4_M M_G1C4H1_M": NaN, + "M_G1C4_M M_G1C4H2_M": NaN, + "M_G1C5_M M_G1C5H1_M": NaN, + "M_G1C5_M M_G1C5H2_M": NaN, + "M_G1C6_M M_G1C6H1_M": NaN, + "M_G1C6_M M_G1C6H2_M": NaN, + "M_G1C7_M M_G1C7H1_M": NaN, + "M_G1C7_M M_G1C7H2_M": NaN, + "M_G1C8_M M_G1C8H1_M": NaN, + "M_G1C8_M M_G1C8H2_M": NaN, + "M_G1C9_M M_G1C9H1_M": NaN, + "M_G1C9_M M_G1C9H2_M": NaN, + "M_G1_M M_G1H1_M": NaN, + "M_G1_M M_G1H2_M": NaN, + "M_G2C10_M M_G2C10H1_M": NaN, + "M_G2C10_M M_G2C10H2_M": NaN, + "M_G2C11_M M_G2C11H1_M": NaN, + "M_G2C11_M M_G2C11H2_M": NaN, + "M_G2C12_M M_G2C12H1_M": NaN, + "M_G2C12_M M_G2C12H2_M": NaN, + "M_G2C13_M M_G2C13H1_M": NaN, + "M_G2C13_M M_G2C13H2_M": NaN, + "M_G2C14_M M_G2C14H1_M": NaN, + "M_G2C14_M M_G2C14H2_M": NaN, + "M_G2C15_M M_G2C15H1_M": NaN, + "M_G2C15_M M_G2C15H2_M": NaN, + "M_G2C16_M M_G2C16H1_M": NaN, + "M_G2C16_M M_G2C16H2_M": NaN, + "M_G2C17_M M_G2C17H1_M": NaN, + "M_G2C17_M M_G2C17H2_M": NaN, + "M_G2C17_M M_G2C17H3_M": NaN, + "M_G2C3_M M_G2C3H1_M": NaN, + "M_G2C3_M M_G2C3H2_M": NaN, + "M_G2C4_M M_G2C4H1_M": NaN, + "M_G2C4_M M_G2C4H2_M": NaN, + "M_G2C5_M M_G2C5H1_M": NaN, + "M_G2C5_M M_G2C5H2_M": NaN, + "M_G2C6_M M_G2C6H1_M": NaN, + "M_G2C6_M M_G2C6H2_M": NaN, + "M_G2C7_M M_G2C7H1_M": NaN, + "M_G2C7_M M_G2C7H2_M": NaN, + "M_G2C8_M M_G2C8H1_M": NaN, + "M_G2C8_M M_G2C8H2_M": NaN, + "M_G2C9_M M_G2C9H1_M": NaN, + "M_G2C9_M M_G2C9H2_M": NaN, + "M_G2_M M_G2H1_M": NaN, + "M_G3C4_M M_G3C4H1_M": 0.083, + "M_G3C4_M M_G3C4H2_M": 0.0737, + "M_G3C5_M M_G3C5H1_M": 0.4601, + "M_G3C5_M M_G3C5H2_M": 0.3097, + "M_G3N6C1_M M_G3N6C1H1_M": 0.9851, + "M_G3N6C1_M M_G3N6C1H2_M": 0.9864, + "M_G3N6C1_M M_G3N6C1H3_M": 0.9871, + "M_G3N6C2_M M_G3N6C2H1_M": 0.9857, + "M_G3N6C2_M M_G3N6C2H2_M": 0.9869, + "M_G3N6C2_M M_G3N6C2H3_M": 0.9856, + "M_G3N6C3_M M_G3N6C3H1_M": 0.9859, + "M_G3N6C3_M M_G3N6C3H2_M": 0.9858, + "M_G3N6C3_M M_G3N6C3H3_M": 0.9868, + "M_G3_M M_G3H1_M": 0.7344, + "M_G3_M M_G3H2_M": 0.4768 + } +} \ No newline at end of file diff --git a/Simulations/670/484/6704849a21596a96b4e490419f3c937d719b2904/718296d4c5b00da31a47037e847ab0d5c5246d2c/README.yaml b/Simulations/670/484/6704849a21596a96b4e490419f3c937d719b2904/718296d4c5b00da31a47037e847ab0d5c5246d2c/README.yaml index f83c422792..468cc55ce4 100644 --- a/Simulations/670/484/6704849a21596a96b4e490419f3c937d719b2904/718296d4c5b00da31a47037e847ab0d5c5246d2c/README.yaml +++ b/Simulations/670/484/6704849a21596a96b4e490419f3c937d719b2904/718296d4c5b00da31a47037e847ab0d5c5246d2c/README.yaml @@ -39,3 +39,8 @@ NUMBER_OF_ATOMS: 53000 DATEOFRUNNING: 15/09/2026 TYPEOFSYSTEM: lipid bilayer ID: 933 +EXPERIMENT: + ORDERPARAMETER: + DPPC: + - 10.1021/bi00687a021/1 + FORMFACTOR: [] diff --git a/Simulations/670/484/6704849a21596a96b4e490419f3c937d719b2904/718296d4c5b00da31a47037e847ab0d5c5246d2c/SYSTEM_quality.json b/Simulations/670/484/6704849a21596a96b4e490419f3c937d719b2904/718296d4c5b00da31a47037e847ab0d5c5246d2c/SYSTEM_quality.json new file mode 100644 index 0000000000..fe09aab50b --- /dev/null +++ b/Simulations/670/484/6704849a21596a96b4e490419f3c937d719b2904/718296d4c5b00da31a47037e847ab0d5c5246d2c/SYSTEM_quality.json @@ -0,0 +1 @@ +{"headgroup": 0.6118, "tails": 0.0, "total": 0.6118} \ No newline at end of file diff --git a/Simulations/671/199/671199c998a93dcf594469ea33e3b25e73d08b9e/25bf45d5d477c8ae86de3b9c044ead9489d678f6/README.yaml b/Simulations/671/199/671199c998a93dcf594469ea33e3b25e73d08b9e/25bf45d5d477c8ae86de3b9c044ead9489d678f6/README.yaml index 615ca700fd..fd7e96586d 100644 --- a/Simulations/671/199/671199c998a93dcf594469ea33e3b25e73d08b9e/25bf45d5d477c8ae86de3b9c044ead9489d678f6/README.yaml +++ b/Simulations/671/199/671199c998a93dcf594469ea33e3b25e73d08b9e/25bf45d5d477c8ae86de3b9c044ead9489d678f6/README.yaml @@ -64,9 +64,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 601 bioschema_properties: - name: Molecular dynamics trajectory of a CLA/DMPC/DMTAP/SOD (35:30:30:5) bilayer at 323 K (Berger with DMTAP modification by Gurtovenko et al., GROMACS 3.x, 190 ns) [NMRlipids simulation 601] + name: Molecular dynamics trajectory of a CLA/DMPC/DMTAP/SOD (35:30:30:5) bilayer + at 323 K (Berger with DMTAP modification by Gurtovenko et al., GROMACS 3.x, 190 + ns) [NMRlipids simulation 601] alternateName: 64DMPC_64DMTAP_10SOD_74CLA_5316SOL_323K - description: Molecular dynamics trajectory of a lipid bilayer of 74 CLA (35 mol%), 64 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine, 30 mol%), 64 DMTAP (1,2-dimyristoyl-3-trimethylammonium-propane, 30 mol%) and 10 SOD (5 mol%) at 323 K. Simulated with Berger with DMTAP modification by Gurtovenko et al. in GROMACS 3.x for 190 ns (21472 atoms). Deposited as NMRlipids Databank simulation 601 and available from https://doi.org/10.5281/zenodo.53212. + description: Molecular dynamics trajectory of a lipid bilayer of 74 CLA (35 mol%), + 64 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine, 30 mol%), 64 DMTAP (1,2-dimyristoyl-3-trimethylammonium-propane, + 30 mol%) and 10 SOD (5 mol%) at 323 K. Simulated with Berger with DMTAP modification + by Gurtovenko et al. in GROMACS 3.x for 190 ns (21472 atoms). Deposited as NMRlipids + Databank simulation 601 and available from https://doi.org/10.5281/zenodo.53212. sameAs: https://doi.org/10.5281/zenodo.53212 datePublished: '2016-05-27' license: @@ -165,7 +171,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.53212 identifier: 10.5281/zenodo.53212 url: https://doi.org/10.5281/zenodo.53212 - name: 'Molecular dynamics simulation trajectory of a cationic lipid bilayer: 50/50 mol% DMTAP/DMPC in 0.1 M NaCl' + name: 'Molecular dynamics simulation trajectory of a cationic lipid bilayer: 50/50 + mol% DMTAP/DMPC in 0.1 M NaCl' publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/680/3e0/6803e029dcdfd8b4017e7a40f2e6d7aed83ff1f0/29fb6fe76805a1f4450ae629341118b94756457c/README.yaml b/Simulations/680/3e0/6803e029dcdfd8b4017e7a40f2e6d7aed83ff1f0/29fb6fe76805a1f4450ae629341118b94756457c/README.yaml index b0c6f53c4b..54b2409daa 100644 --- a/Simulations/680/3e0/6803e029dcdfd8b4017e7a40f2e6d7aed83ff1f0/29fb6fe76805a1f4450ae629341118b94756457c/README.yaml +++ b/Simulations/680/3e0/6803e029dcdfd8b4017e7a40f2e6d7aed83ff1f0/29fb6fe76805a1f4450ae629341118b94756457c/README.yaml @@ -41,9 +41,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 477 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 303 K (GAFFlipid, GROMACS 4.5, 42 ns) [NMRlipids simulation 477] + name: Molecular dynamics trajectory of a POPC bilayer at 303 K (GAFFlipid, GROMACS + 4.5, 42 ns) [NMRlipids simulation 477] alternateName: 126POPC_896SOL_303K - description: Molecular dynamics trajectory of a lipid bilayer of 126 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 303 K. Simulated with GAFFlipid in GROMACS 4.5 for 42 ns (19572 atoms). Deposited as NMRlipids Databank simulation 477 and available from https://doi.org/10.5281/zenodo.13853. + description: Molecular dynamics trajectory of a lipid bilayer of 126 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 303 K. Simulated with GAFFlipid in GROMACS 4.5 for 42 ns (19572 atoms). Deposited + as NMRlipids Databank simulation 477 and available from https://doi.org/10.5281/zenodo.13853. sameAs: https://doi.org/10.5281/zenodo.13853 datePublished: '2015-01-09' license: @@ -131,7 +134,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.13853 identifier: 10.5281/zenodo.13853 url: https://doi.org/10.5281/zenodo.13853 - name: Md Simulation Trajectory And Related Files For Popc Bilayer In Low Hydration (Gafflipid, Gromacs 4.5) + name: Md Simulation Trajectory And Related Files For Popc Bilayer In Low Hydration + (Gafflipid, Gromacs 4.5) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/681/e46/681e462b5562cb21fc7481562e54093e3f9bfead/d85c48d4263e1b357b0c213b720a0b842f7647de/README.yaml b/Simulations/681/e46/681e462b5562cb21fc7481562e54093e3f9bfead/d85c48d4263e1b357b0c213b720a0b842f7647de/README.yaml index 9fe18b07e0..83f3bb79f8 100644 --- a/Simulations/681/e46/681e462b5562cb21fc7481562e54093e3f9bfead/d85c48d4263e1b357b0c213b720a0b842f7647de/README.yaml +++ b/Simulations/681/e46/681e462b5562cb21fc7481562e54093e3f9bfead/d85c48d4263e1b357b0c213b720a0b842f7647de/README.yaml @@ -44,9 +44,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 44 bioschema_properties: - name: Molecular dynamics trajectory of a DOPE bilayer at 271 K (GROMOS-CKP, GROMACS 5.0.6, 400 ns) [NMRlipids simulation 44] + name: Molecular dynamics trajectory of a DOPE bilayer at 271 K (GROMOS-CKP, GROMACS + 5.0.6, 400 ns) [NMRlipids simulation 44] alternateName: 128DOPE_4789SOL_271K_GROMOS-CKP_v2 - description: Molecular dynamics trajectory of a lipid bilayer of 128 DOPE (1,2-dioleoyl-sn-glycero-3-phosphoethanolamine) at 271 K. Simulated with GROMOS-CKP in GROMACS 5.0.6 for 400 ns (21279 atoms). Deposited as NMRlipids Databank simulation 44 and available from https://doi.org/10.5281/zenodo.1293941. + description: Molecular dynamics trajectory of a lipid bilayer of 128 DOPE (1,2-dioleoyl-sn-glycero-3-phosphoethanolamine) + at 271 K. Simulated with GROMOS-CKP in GROMACS 5.0.6 for 400 ns (21279 atoms). + Deposited as NMRlipids Databank simulation 44 and available from https://doi.org/10.5281/zenodo.1293941. sameAs: https://doi.org/10.5281/zenodo.1293941 datePublished: '2018-06-20' license: diff --git a/Simulations/687/d2d/687d2d5cfca70fea15e0cf229f00788f9d1d5bb1/8f3ccb5c63811beffd853c495783b324a7ec4052/README.yaml b/Simulations/687/d2d/687d2d5cfca70fea15e0cf229f00788f9d1d5bb1/8f3ccb5c63811beffd853c495783b324a7ec4052/README.yaml index f1bec1c0e2..ae2542ad04 100644 --- a/Simulations/687/d2d/687d2d5cfca70fea15e0cf229f00788f9d1d5bb1/8f3ccb5c63811beffd853c495783b324a7ec4052/README.yaml +++ b/Simulations/687/d2d/687d2d5cfca70fea15e0cf229f00788f9d1d5bb1/8f3ccb5c63811beffd853c495783b324a7ec4052/README.yaml @@ -49,9 +49,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 159 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (48:35:17) bilayer at 310.15 K (CHARMM36, GROMACS 5.0, 2000 ns) [NMRlipids simulation 159] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (48:35:17) bilayer at 310.15 + K (CHARMM36, GROMACS 5.0, 2000 ns) [NMRlipids simulation 159] alternateName: 200POPC_9000SOL_73CAL_146CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 48 mol%), 146 CLA (35 mol%) and 73 CAL (17 mol%) at 310.15 K. Simulated with CHARMM36 in GROMACS 5.0 for 2000 ns (54019 atoms). Deposited as NMRlipids Databank simulation 159 and available from https://doi.org/10.5281/zenodo.259365. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 48 mol%), 146 CLA (35 mol%) and 73 CAL (17 mol%) at 310.15 K. Simulated with CHARMM36 + in GROMACS 5.0 for 2000 ns (54019 atoms). Deposited as NMRlipids Databank simulation + 159 and available from https://doi.org/10.5281/zenodo.259365. sameAs: https://doi.org/10.5281/zenodo.259365 datePublished: '2017-01-24' license: @@ -139,7 +143,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.259365 identifier: 10.5281/zenodo.259365 url: https://doi.org/10.5281/zenodo.259365 - name: Popc With Varying Amounts Of Cholesterol, 450 Mm Of Cacl_2. Charmm36 With Default Charmm Ions + name: Popc With Varying Amounts Of Cholesterol, 450 Mm Of Cacl_2. Charmm36 With + Default Charmm Ions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/687/d2d/687d2d5cfca70fea15e0cf229f00788f9d1d5bb1/de59670e86fb0ac7706ddd4a0d447411b53dd810/README.yaml b/Simulations/687/d2d/687d2d5cfca70fea15e0cf229f00788f9d1d5bb1/de59670e86fb0ac7706ddd4a0d447411b53dd810/README.yaml index 4844ff7d8b..184e125855 100644 --- a/Simulations/687/d2d/687d2d5cfca70fea15e0cf229f00788f9d1d5bb1/de59670e86fb0ac7706ddd4a0d447411b53dd810/README.yaml +++ b/Simulations/687/d2d/687d2d5cfca70fea15e0cf229f00788f9d1d5bb1/de59670e86fb0ac7706ddd4a0d447411b53dd810/README.yaml @@ -49,9 +49,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 160 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (48:35:17) bilayer at 310.15 K (CHARMM36, GROMACS, 100 ns) [NMRlipids simulation 160] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (48:35:17) bilayer at 310.15 + K (CHARMM36, GROMACS, 100 ns) [NMRlipids simulation 160] alternateName: 200POPC_9000SOL_73CAL_146CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 48 mol%), 146 CLA (35 mol%) and 73 CAL (17 mol%) at 310.15 K. Simulated with CHARMM36 in GROMACS for 100 ns (54019 atoms). Deposited as NMRlipids Databank simulation 160 and available from https://doi.org/10.5281/zenodo.51185. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 48 mol%), 146 CLA (35 mol%) and 73 CAL (17 mol%) at 310.15 K. Simulated with CHARMM36 + in GROMACS for 100 ns (54019 atoms). Deposited as NMRlipids Databank simulation + 160 and available from https://doi.org/10.5281/zenodo.51185. sameAs: https://doi.org/10.5281/zenodo.51185 datePublished: '2016-05-09' license: diff --git a/Simulations/687/d70/687d70e3855bd3ed984fda6baeef96d42ba9126d/78ba0e56b430751678b07c2665a17c17b64203e6/README.yaml b/Simulations/687/d70/687d70e3855bd3ed984fda6baeef96d42ba9126d/78ba0e56b430751678b07c2665a17c17b64203e6/README.yaml index b9d270ad1f..90ea321931 100644 --- a/Simulations/687/d70/687d70e3855bd3ed984fda6baeef96d42ba9126d/78ba0e56b430751678b07c2665a17c17b64203e6/README.yaml +++ b/Simulations/687/d70/687d70e3855bd3ed984fda6baeef96d42ba9126d/78ba0e56b430751678b07c2665a17c17b64203e6/README.yaml @@ -50,9 +50,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/3 ID: 665 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (89:11) bilayer at 298.15 K (MacRog, GROMACS 2021, 1001 ns) [NMRlipids simulation 665] + name: Molecular dynamics trajectory of a POPC/CHOL (89:11) bilayer at 298.15 K (MacRog, + GROMACS 2021, 1001 ns) [NMRlipids simulation 665] alternateName: MacRog_POPC_CHOL11_S - description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 89 mol%) and 8 CHOL (cholesterol, 11 mol%) at 298.15 K. Simulated with MacRog in GROMACS 2021 for 1001 ns (19968 atoms). Deposited as NMRlipids Databank simulation 665 and available from https://doi.org/10.5281/zenodo.7061800. + description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 89 mol%) and 8 CHOL (cholesterol, 11 mol%) at 298.15 K. Simulated with MacRog + in GROMACS 2021 for 1001 ns (19968 atoms). Deposited as NMRlipids Databank simulation + 665 and available from https://doi.org/10.5281/zenodo.7061800. sameAs: https://doi.org/10.5281/zenodo.7061800 datePublished: '2022-09-08' license: diff --git a/Simulations/68d/39e/68d39e96aca23aeaa4ea2567e0e0cb8b8903a694/68d39e96aca23aeaa4ea2567e0e0cb8b8903a694/README.yaml b/Simulations/68d/39e/68d39e96aca23aeaa4ea2567e0e0cb8b8903a694/68d39e96aca23aeaa4ea2567e0e0cb8b8903a694/README.yaml index bcbbbccdf1..29b26754a5 100644 --- a/Simulations/68d/39e/68d39e96aca23aeaa4ea2567e0e0cb8b8903a694/68d39e96aca23aeaa4ea2567e0e0cb8b8903a694/README.yaml +++ b/Simulations/68d/39e/68d39e96aca23aeaa4ea2567e0e0cb8b8903a694/68d39e96aca23aeaa4ea2567e0e0cb8b8903a694/README.yaml @@ -41,9 +41,12 @@ EXPERIMENT: FORMFACTOR: - 10.1021/acs.jpcb.0c03389/2 bioschema_properties: - name: Molecular dynamics trajectory of a SM16 bilayer at 328.15 K (Charmm36, NAMD, 0 ns) [NMRlipids simulation 765] + name: Molecular dynamics trajectory of a SM16 bilayer at 328.15 K (Charmm36, NAMD, + 0 ns) [NMRlipids simulation 765] alternateName: PSM NAMD - description: Molecular dynamics trajectory of a lipid bilayer of 200 SM16 (N-palmitoyl-D-erythro-sphingosylphosphorylcholine) at 328.15 K. Simulated with Charmm36 in NAMD for 0 ns (52400 atoms). Deposited as NMRlipids Databank simulation 765 and available from https://doi.org/10.5281/zenodo.8338253. + description: Molecular dynamics trajectory of a lipid bilayer of 200 SM16 (N-palmitoyl-D-erythro-sphingosylphosphorylcholine) + at 328.15 K. Simulated with Charmm36 in NAMD for 0 ns (52400 atoms). Deposited + as NMRlipids Databank simulation 765 and available from https://doi.org/10.5281/zenodo.8338253. sameAs: https://doi.org/10.5281/zenodo.8338253 datePublished: '2023-09-12' license: diff --git a/Simulations/692/0a3/6920a30724aaee777ec0b58cbcf374950e2f8c5a/a9d3cacb63c4303cc7ede19f21c58b8550e47b04/README.yaml b/Simulations/692/0a3/6920a30724aaee777ec0b58cbcf374950e2f8c5a/a9d3cacb63c4303cc7ede19f21c58b8550e47b04/README.yaml index 4a6b6a7c15..3808258274 100644 --- a/Simulations/692/0a3/6920a30724aaee777ec0b58cbcf374950e2f8c5a/a9d3cacb63c4303cc7ede19f21c58b8550e47b04/README.yaml +++ b/Simulations/692/0a3/6920a30724aaee777ec0b58cbcf374950e2f8c5a/a9d3cacb63c4303cc7ede19f21c58b8550e47b04/README.yaml @@ -49,9 +49,12 @@ WARNINGS: TIMESTEP: incorrect ID: 805 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 300 K (OPLS3e, GROMACS Desmond 2019-4, 500 ns) [NMRlipids simulation 805] + name: Molecular dynamics trajectory of a POPC bilayer at 300 K (OPLS3e, GROMACS + Desmond 2019-4, 500 ns) [NMRlipids simulation 805] alternateName: 200POPC_8859SOL_300K_run_with_demond_convert_gromacs - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 300 K. Simulated with OPLS3e in GROMACS Desmond 2019-4 for 500 ns (53377 atoms). Deposited as NMRlipids Databank simulation 805 and available from https://doi.org/10.5281/zenodo.10183982. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 300 K. Simulated with OPLS3e in GROMACS Desmond 2019-4 for 500 ns (53377 atoms). + Deposited as NMRlipids Databank simulation 805 and available from https://doi.org/10.5281/zenodo.10183982. sameAs: https://doi.org/10.5281/zenodo.10183982 datePublished: '2022' license: @@ -142,7 +145,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.10183982 identifier: 10.5281/zenodo.10183982 url: https://doi.org/10.5281/zenodo.10183982 - name: MD simulation of POPC bilayer with OPLS3e force field. Full hydration 44 w/l + name: MD simulation of POPC bilayer with OPLS3e force field. Full hydration 44 + w/l publisher: Zenodo _source: api: datacite diff --git a/Simulations/697/389/697389ca7f8b33d3ae993011b4dce90552673236/0e844489f156b3fd6da79acdd207a613ebcd2346/README.yaml b/Simulations/697/389/697389ca7f8b33d3ae993011b4dce90552673236/0e844489f156b3fd6da79acdd207a613ebcd2346/README.yaml index 8f2556cba3..26176a9e39 100644 --- a/Simulations/697/389/697389ca7f8b33d3ae993011b4dce90552673236/0e844489f156b3fd6da79acdd207a613ebcd2346/README.yaml +++ b/Simulations/697/389/697389ca7f8b33d3ae993011b4dce90552673236/0e844489f156b3fd6da79acdd207a613ebcd2346/README.yaml @@ -50,9 +50,13 @@ SOFTWARE: gromacs DIR_WRK: /usr/home/bort/Databank ID: 315 bioschema_properties: - name: Molecular dynamics trajectory of a DLIPC/CHOL (90:10) bilayer at 310 K (CHARMM36, GROMACS, 1000 ns) [NMRlipids simulation 315] + name: Molecular dynamics trajectory of a DLIPC/CHOL (90:10) bilayer at 310 K (CHARMM36, + GROMACS, 1000 ns) [NMRlipids simulation 315] alternateName: 260DLIPC_28CHOL_11520SOL_310K - description: Molecular dynamics trajectory of a lipid bilayer of 260 DLIPC (1,2-dilinoleoyl-sn-glycero-3-phosphocholine, 90 mol%) and 28 CHOL (cholesterol, 10 mol%) at 310 K. Simulated with CHARMM36 in GROMACS for 1000 ns (71472 atoms). Deposited as NMRlipids Databank simulation 315 and available from https://doi.org/10.5281/zenodo.2653721. + description: Molecular dynamics trajectory of a lipid bilayer of 260 DLIPC (1,2-dilinoleoyl-sn-glycero-3-phosphocholine, + 90 mol%) and 28 CHOL (cholesterol, 10 mol%) at 310 K. Simulated with CHARMM36 + in GROMACS for 1000 ns (71472 atoms). Deposited as NMRlipids Databank simulation + 315 and available from https://doi.org/10.5281/zenodo.2653721. sameAs: https://doi.org/10.5281/zenodo.2653721 datePublished: '2019-04-29' license: @@ -141,7 +145,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.2653721 identifier: 10.5281/zenodo.2653721 url: https://doi.org/10.5281/zenodo.2653721 - name: Atomistic simulations of cholesterol in symmetric lipid bilayers with varying degrees of lipid chain unsaturation + name: Atomistic simulations of cholesterol in symmetric lipid bilayers with varying + degrees of lipid chain unsaturation publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/699/c14/699c14edee844ced21aedbcec30649979bf8121c/ab8576d84d0ea717a66d042aeac5195b4d8750cc/README.yaml b/Simulations/699/c14/699c14edee844ced21aedbcec30649979bf8121c/ab8576d84d0ea717a66d042aeac5195b4d8750cc/README.yaml index 8efd0a085d..84542b3d92 100644 --- a/Simulations/699/c14/699c14edee844ced21aedbcec30649979bf8121c/ab8576d84d0ea717a66d042aeac5195b4d8750cc/README.yaml +++ b/Simulations/699/c14/699c14edee844ced21aedbcec30649979bf8121c/ab8576d84d0ea717a66d042aeac5195b4d8750cc/README.yaml @@ -50,9 +50,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/5 ID: 666 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (80:20) bilayer at 298.15 K (Lipid17, GROMACS 2021, 1001 ns) [NMRlipids simulation 666] + name: Molecular dynamics trajectory of a POPC/CHOL (80:20) bilayer at 298.15 K (Lipid17, + GROMACS 2021, 1001 ns) [NMRlipids simulation 666] alternateName: Lipid17_POPC_CHOL20_M - description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 80 mol%) and 64 CHOL (cholesterol, 20 mol%) at 298.15 K. Simulated with Lipid17 in GROMACS 2021 for 1001 ns (87040 atoms). Deposited as NMRlipids Databank simulation 666 and available from https://doi.org/10.5281/zenodo.6992065. + description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 80 mol%) and 64 CHOL (cholesterol, 20 mol%) at 298.15 K. Simulated with Lipid17 + in GROMACS 2021 for 1001 ns (87040 atoms). Deposited as NMRlipids Databank simulation + 666 and available from https://doi.org/10.5281/zenodo.6992065. sameAs: https://doi.org/10.5281/zenodo.6992065 datePublished: '2022-08-15' license: diff --git a/Simulations/6a1/bbc/6a1bbc478e03fca6d1567f3d9451cfe5c8aadc72/6a1bbc478e03fca6d1567f3d9451cfe5c8aadc72/README.yaml b/Simulations/6a1/bbc/6a1bbc478e03fca6d1567f3d9451cfe5c8aadc72/6a1bbc478e03fca6d1567f3d9451cfe5c8aadc72/README.yaml index 5f31948acb..52966fa71d 100644 --- a/Simulations/6a1/bbc/6a1bbc478e03fca6d1567f3d9451cfe5c8aadc72/6a1bbc478e03fca6d1567f3d9451cfe5c8aadc72/README.yaml +++ b/Simulations/6a1/bbc/6a1bbc478e03fca6d1567f3d9451cfe5c8aadc72/6a1bbc478e03fca6d1567f3d9451cfe5c8aadc72/README.yaml @@ -43,9 +43,12 @@ EXPERIMENT: FORMFACTOR: - 10.1021/jp511159q/1 bioschema_properties: - name: Molecular dynamics trajectory of a POPE bilayer at 308 K (Charmm-Drude polarizable2023, OPENMM, 200 ns) [NMRlipids simulation 750] + name: Molecular dynamics trajectory of a POPE bilayer at 308 K (Charmm-Drude polarizable2023, + OPENMM, 200 ns) [NMRlipids simulation 750] alternateName: POPE_CHARMMdrude2023_308K - description: Molecular dynamics trajectory of a lipid bilayer of 72 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) at 308 K. Simulated with Charmm-Drude polarizable2023 in OPENMM for 200 ns (24624 atoms). Deposited as NMRlipids Databank simulation 750 and available from https://doi.org/10.5281/zenodo.7916494. + description: Molecular dynamics trajectory of a lipid bilayer of 72 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) + at 308 K. Simulated with Charmm-Drude polarizable2023 in OPENMM for 200 ns (24624 + atoms). Deposited as NMRlipids Databank simulation 750 and available from https://doi.org/10.5281/zenodo.7916494. sameAs: https://doi.org/10.5281/zenodo.7916494 datePublished: '2023-05-09' license: @@ -135,7 +138,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.7916494 identifier: 10.5281/zenodo.7916494 url: https://doi.org/10.5281/zenodo.7916494 - name: OpenMM simulations of POPE using the CHARMM Drude2023 force field in xtc format + name: OpenMM simulations of POPE using the CHARMM Drude2023 force field in xtc + format publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/6a7/ee8/6a7ee8ec651f41dbaa4460d095ad2e30b27de20b/9b33210b33f94f175df15b16f5064d9464900b05/README.yaml b/Simulations/6a7/ee8/6a7ee8ec651f41dbaa4460d095ad2e30b27de20b/9b33210b33f94f175df15b16f5064d9464900b05/README.yaml index cd44ba72ec..469834749d 100644 --- a/Simulations/6a7/ee8/6a7ee8ec651f41dbaa4460d095ad2e30b27de20b/9b33210b33f94f175df15b16f5064d9464900b05/README.yaml +++ b/Simulations/6a7/ee8/6a7ee8ec651f41dbaa4460d095ad2e30b27de20b/9b33210b33f94f175df15b16f5064d9464900b05/README.yaml @@ -43,9 +43,12 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/1 ID: 63 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 298 K (MacRog, GROMACS 4.5.5, 40 ns) [NMRlipids simulation 63] + name: Molecular dynamics trajectory of a POPC bilayer at 298 K (MacRog, GROMACS + 4.5.5, 40 ns) [NMRlipids simulation 63] alternateName: 288POPC_14400SOL_298K - description: Molecular dynamics trajectory of a lipid bilayer of 288 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 298 K. Simulated with MacRog in GROMACS 4.5.5 for 40 ns (81792 atoms). Deposited as NMRlipids Databank simulation 63 and available from https://doi.org/10.5281/zenodo.13498. + description: Molecular dynamics trajectory of a lipid bilayer of 288 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 298 K. Simulated with MacRog in GROMACS 4.5.5 for 40 ns (81792 atoms). Deposited + as NMRlipids Databank simulation 63 and available from https://doi.org/10.5281/zenodo.13498. sameAs: https://doi.org/10.5281/zenodo.13498 datePublished: '2014-12-30' license: diff --git a/Simulations/6aa/abe/6aaabefe1ee940b7935eae818066d12be542d388/fbdd612cccaad0dcc7568f40c4e3bbce8d68d074/README.yaml b/Simulations/6aa/abe/6aaabefe1ee940b7935eae818066d12be542d388/fbdd612cccaad0dcc7568f40c4e3bbce8d68d074/README.yaml index b6578ee4db..f7fc73665c 100644 --- a/Simulations/6aa/abe/6aaabefe1ee940b7935eae818066d12be542d388/fbdd612cccaad0dcc7568f40c4e3bbce8d68d074/README.yaml +++ b/Simulations/6aa/abe/6aaabefe1ee940b7935eae818066d12be542d388/fbdd612cccaad0dcc7568f40c4e3bbce8d68d074/README.yaml @@ -51,9 +51,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 157 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (48:35:17) bilayer at 298 K (Orange, GROMACS 4.5, 60 ns) [NMRlipids simulation 157] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (48:35:17) bilayer at 298 + K (Orange, GROMACS 4.5, 60 ns) [NMRlipids simulation 157] alternateName: 72POPC_2802SOL_52CLA_26CAL_298K - description: Molecular dynamics trajectory of a lipid bilayer of 72 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 48 mol%), 52 CLA (35 mol%) and 26 CAL (17 mol%) at 298 K. Simulated with Orange in GROMACS 4.5 for 60 ns (12228 atoms). Deposited as NMRlipids Databank simulation 157 and available from https://doi.org/10.5281/zenodo.34498. + description: Molecular dynamics trajectory of a lipid bilayer of 72 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 48 mol%), 52 CLA (35 mol%) and 26 CAL (17 mol%) at 298 K. Simulated with Orange + in GROMACS 4.5 for 60 ns (12228 atoms). Deposited as NMRlipids Databank simulation + 157 and available from https://doi.org/10.5281/zenodo.34498. sameAs: https://doi.org/10.5281/zenodo.34498 datePublished: '2015-12-02' license: @@ -142,7 +146,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.34498 identifier: 10.5281/zenodo.34498 url: https://doi.org/10.5281/zenodo.34498 - name: Md Simulation Trajectory For Popc Bilayer With 510Mm Cacl_2 (Orange, Gromacs 4.5.) + name: Md Simulation Trajectory For Popc Bilayer With 510Mm Cacl_2 (Orange, Gromacs + 4.5.) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/6ad/2f4/6ad2f424e379b04974972623cde5e2da181bcb15/5370e6e9155fd2d823114a4efb383ed52f44c71c/README.yaml b/Simulations/6ad/2f4/6ad2f424e379b04974972623cde5e2da181bcb15/5370e6e9155fd2d823114a4efb383ed52f44c71c/README.yaml index d16add7bda..31dd26cfe1 100644 --- a/Simulations/6ad/2f4/6ad2f424e379b04974972623cde5e2da181bcb15/5370e6e9155fd2d823114a4efb383ed52f44c71c/README.yaml +++ b/Simulations/6ad/2f4/6ad2f424e379b04974972623cde5e2da181bcb15/5370e6e9155fd2d823114a4efb383ed52f44c71c/README.yaml @@ -55,9 +55,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 243 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/CLA/SOD (82:9:9) bilayer at 323 K (Berger-DPPC-98, GROMACS 5.0.4, 120 ns) [NMRlipids simulation 243] + name: Molecular dynamics trajectory of a DPPC/CLA/SOD (82:9:9) bilayer at 323 K + (Berger-DPPC-98, GROMACS 5.0.4, 120 ns) [NMRlipids simulation 243] alternateName: 72DPPC_2864SOL_8SOD_8CLA_323K - description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 82 mol%), 8 CLA (9 mol%) and 8 SOD (9 mol%) at 323 K. Simulated with Berger-DPPC-98 in GROMACS 5.0.4 for 120 ns (12208 atoms). Deposited as NMRlipids Databank simulation 243 and available from https://doi.org/10.5281/zenodo.16319. + description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 82 mol%), 8 CLA (9 mol%) and 8 SOD (9 mol%) at 323 K. Simulated with Berger-DPPC-98 + in GROMACS 5.0.4 for 120 ns (12208 atoms). Deposited as NMRlipids Databank simulation + 243 and available from https://doi.org/10.5281/zenodo.16319. sameAs: https://doi.org/10.5281/zenodo.16319 datePublished: '2015-03-24' license: diff --git a/Simulations/6b1/a92/6b1a92a12890e9268c68737792b76d286dfb3da7/d888eb331e20b6592163e4911c4160192868e2a1/README.yaml b/Simulations/6b1/a92/6b1a92a12890e9268c68737792b76d286dfb3da7/d888eb331e20b6592163e4911c4160192868e2a1/README.yaml index dc3a5132b0..89d69292c1 100644 --- a/Simulations/6b1/a92/6b1a92a12890e9268c68737792b76d286dfb3da7/d888eb331e20b6592163e4911c4160192868e2a1/README.yaml +++ b/Simulations/6b1/a92/6b1a92a12890e9268c68737792b76d286dfb3da7/d888eb331e20b6592163e4911c4160192868e2a1/README.yaml @@ -51,9 +51,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 841 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (85:8:8) bilayer at 310 K (prosECCo75, GROMACS, 1000 ns) [NMRlipids simulation 841] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (85:8:8) bilayer at 310 K + (prosECCo75, GROMACS, 1000 ns) [NMRlipids simulation 841] alternateName: POPC_113mM_NaCl_prosECCo75 - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 85 mol%), 18 CLA (8 mol%) and 18 SOD (8 mol%) at 310 K. Simulated with prosECCo75 in GROMACS for 1000 ns (53836 atoms). Deposited as NMRlipids Databank simulation 841 and available from https://doi.org/10.5281/zenodo.10464960. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 85 mol%), 18 CLA (8 mol%) and 18 SOD (8 mol%) at 310 K. Simulated with prosECCo75 + in GROMACS for 1000 ns (53836 atoms). Deposited as NMRlipids Databank simulation + 841 and available from https://doi.org/10.5281/zenodo.10464960. sameAs: https://doi.org/10.5281/zenodo.10464960 datePublished: '2024-01-06' license: diff --git a/Simulations/6b5/4ba/6b54babd957323afe3ae35bb541e90f10bdceaa9/fc1fac7ee089ef5742c724e8375ca833eedd88c0/README.yaml b/Simulations/6b5/4ba/6b54babd957323afe3ae35bb541e90f10bdceaa9/fc1fac7ee089ef5742c724e8375ca833eedd88c0/README.yaml index 64dc273ea8..57da01e254 100644 --- a/Simulations/6b5/4ba/6b54babd957323afe3ae35bb541e90f10bdceaa9/fc1fac7ee089ef5742c724e8375ca833eedd88c0/README.yaml +++ b/Simulations/6b5/4ba/6b54babd957323afe3ae35bb541e90f10bdceaa9/fc1fac7ee089ef5742c724e8375ca833eedd88c0/README.yaml @@ -50,9 +50,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 862 bioschema_properties: - name: Molecular dynamics trajectory of a CLA/POPC/CAL (47:30:23) bilayer at 300 K (CHARMM36, GROMACS 2019.5, 100 ns) [NMRlipids simulation 862] + name: Molecular dynamics trajectory of a CLA/POPC/CAL (47:30:23) bilayer at 300 + K (CHARMM36, GROMACS 2019.5, 100 ns) [NMRlipids simulation 862] alternateName: POPC, 44 w/l, 300 K, 1 M CaCl2 - description: Molecular dynamics trajectory of a lipid bilayer of 316 CLA (47 mol%), 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 30 mol%) and 158 CAL (23 mol%) at 300 K. Simulated with CHARMM36 in GROMACS 2019.5 for 100 ns (53452 atoms). Deposited as NMRlipids Databank simulation 862 and available from https://doi.org/10.5281/zenodo.6337490. + description: Molecular dynamics trajectory of a lipid bilayer of 316 CLA (47 mol%), + 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 30 mol%) and 158 CAL + (23 mol%) at 300 K. Simulated with CHARMM36 in GROMACS 2019.5 for 100 ns (53452 + atoms). Deposited as NMRlipids Databank simulation 862 and available from https://doi.org/10.5281/zenodo.6337490. sameAs: https://doi.org/10.5281/zenodo.6337490 datePublished: '2022-03-08' license: diff --git a/Simulations/6b5/ad8/6b5ad8e17e5694ea6370830c144ac308a5b33e91/edb36d69bcc0dc407b25f74dff8c28dd635e0ae9/README.yaml b/Simulations/6b5/ad8/6b5ad8e17e5694ea6370830c144ac308a5b33e91/edb36d69bcc0dc407b25f74dff8c28dd635e0ae9/README.yaml index c98e8bb196..a029d4d7dc 100644 --- a/Simulations/6b5/ad8/6b5ad8e17e5694ea6370830c144ac308a5b33e91/edb36d69bcc0dc407b25f74dff8c28dd635e0ae9/README.yaml +++ b/Simulations/6b5/ad8/6b5ad8e17e5694ea6370830c144ac308a5b33e91/edb36d69bcc0dc407b25f74dff8c28dd635e0ae9/README.yaml @@ -54,9 +54,13 @@ EXPERIMENT: BOG: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a DMPC/BOG (67:33) bilayer at 303.15 K (Charmm36, GROMACS 2023.2, 500 ns) [NMRlipids simulation 822] + name: Molecular dynamics trajectory of a DMPC/BOG (67:33) bilayer at 303.15 K (Charmm36, + GROMACS 2023.2, 500 ns) [NMRlipids simulation 822] alternateName: DMPC_BOG_1x2_fh - description: Molecular dynamics trajectory of a lipid bilayer of 108 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine, 67 mol%) and 54 BOG (beta-octyl D-glucopyranoside, 33 mol%) at 303.15 K. Simulated with Charmm36 in GROMACS 2023.2 for 500 ns (47694 atoms). Deposited as NMRlipids Databank simulation 822 and available from https://doi.org/10.5281/zenodo.13881447. + description: Molecular dynamics trajectory of a lipid bilayer of 108 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine, + 67 mol%) and 54 BOG (beta-octyl D-glucopyranoside, 33 mol%) at 303.15 K. Simulated + with Charmm36 in GROMACS 2023.2 for 500 ns (47694 atoms). Deposited as NMRlipids + Databank simulation 822 and available from https://doi.org/10.5281/zenodo.13881447. sameAs: https://doi.org/10.5281/zenodo.13881447 datePublished: '2024-10-02' license: diff --git a/Simulations/6c3/ca7/6c3ca7e1ad7705f7acf41f8d4165af31327259f9/77d781e4e8b5f51c484e44cd7b6022f7794bf02d/README.yaml b/Simulations/6c3/ca7/6c3ca7e1ad7705f7acf41f8d4165af31327259f9/77d781e4e8b5f51c484e44cd7b6022f7794bf02d/README.yaml index 7fa18f41f0..a197c4794d 100644 --- a/Simulations/6c3/ca7/6c3ca7e1ad7705f7acf41f8d4165af31327259f9/77d781e4e8b5f51c484e44cd7b6022f7794bf02d/README.yaml +++ b/Simulations/6c3/ca7/6c3ca7e1ad7705f7acf41f8d4165af31327259f9/77d781e4e8b5f51c484e44cd7b6022f7794bf02d/README.yaml @@ -44,9 +44,12 @@ EXPERIMENT: - 10.1016/j.bbamem.2011.07.022/11 ID: 584 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 313 K (Lipid14, GROMACS, 74 ns) [NMRlipids simulation 584] + name: Molecular dynamics trajectory of a POPC bilayer at 313 K (Lipid14, GROMACS, + 74 ns) [NMRlipids simulation 584] alternateName: 72POPC_2234SOL_313K - description: Molecular dynamics trajectory of a lipid bilayer of 72 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 313 K. Simulated with Lipid14 in GROMACS for 74 ns (16350 atoms). Deposited as NMRlipids Databank simulation 584 and available from https://doi.org/10.5281/zenodo.1020709. + description: Molecular dynamics trajectory of a lipid bilayer of 72 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 313 K. Simulated with Lipid14 in GROMACS for 74 ns (16350 atoms). Deposited + as NMRlipids Databank simulation 584 and available from https://doi.org/10.5281/zenodo.1020709. sameAs: https://doi.org/10.5281/zenodo.1020709 datePublished: '2017-10-18' license: diff --git a/Simulations/6cf/f45/6cff4571a9c7abc7c63bf2b03120e2ab90fae508/05a15c5173b98ae86cc569a7567a00ffd9833889/README.yaml b/Simulations/6cf/f45/6cff4571a9c7abc7c63bf2b03120e2ab90fae508/05a15c5173b98ae86cc569a7567a00ffd9833889/README.yaml index 4f1918dc22..9941019337 100644 --- a/Simulations/6cf/f45/6cff4571a9c7abc7c63bf2b03120e2ab90fae508/05a15c5173b98ae86cc569a7567a00ffd9833889/README.yaml +++ b/Simulations/6cf/f45/6cff4571a9c7abc7c63bf2b03120e2ab90fae508/05a15c5173b98ae86cc569a7567a00ffd9833889/README.yaml @@ -88,9 +88,16 @@ EXPERIMENT: GM1: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/POPE/CHOL/CAL/SM16/POPS/GM1 (26:19:16:14:13:6:3:3) bilayer at 300 K (Charmm36, GROMACS 2020.4, 300 ns) [NMRlipids simulation 768] + name: Molecular dynamics trajectory of a POPC/CLA/POPE/CHOL/CAL/SM16/POPS/GM1 (26:19:16:14:13:6:3:3) + bilayer at 300 K (Charmm36, GROMACS 2020.4, 300 ns) [NMRlipids simulation 768] alternateName: POPC_POPE_POPS_SM_CHOL_GM1_CaCl2 - description: Molecular dynamics trajectory of a lipid bilayer of 152 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 26 mol%), 110 CLA (19 mol%), 96 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 16 mol%), 80 CHOL (cholesterol, 14 mol%), 73 CAL (13 mol%), 36 SM16 (N-palmitoyl-D-erythro-sphingosylphosphorylcholine, 6 mol%), 20 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 3 mol%) and 16 GM1 (GM1(d18:1/16:0), 3 mol%) at 300 K. Simulated with Charmm36 in GROMACS 2020.4 for 300 ns (106024 atoms). Deposited as NMRlipids Databank simulation 768 and available from https://doi.org/10.5281/zenodo.8331805. + description: Molecular dynamics trajectory of a lipid bilayer of 152 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 26 mol%), 110 CLA (19 mol%), 96 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, + 16 mol%), 80 CHOL (cholesterol, 14 mol%), 73 CAL (13 mol%), 36 SM16 (N-palmitoyl-D-erythro-sphingosylphosphorylcholine, + 6 mol%), 20 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 3 mol%) + and 16 GM1 (GM1(d18:1/16:0), 3 mol%) at 300 K. Simulated with Charmm36 in GROMACS + 2020.4 for 300 ns (106024 atoms). Deposited as NMRlipids Databank simulation 768 + and available from https://doi.org/10.5281/zenodo.8331805. sameAs: https://doi.org/10.5281/zenodo.8331805 datePublished: '2023-09-10' license: @@ -185,7 +192,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.8331805 identifier: 10.5281/zenodo.8331805 url: https://doi.org/10.5281/zenodo.8331805 - name: MD simulation trajectory for Heterogenous lipid bilayer with 150mM CaCl2 concentration + name: MD simulation trajectory for Heterogenous lipid bilayer with 150mM CaCl2 + concentration publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/6d1/ad4/6d1ad42a2c68788a504632f58d3ab1c982e16742/0b6b528de24dc38b312801853e639b91fbf40b21/README.yaml b/Simulations/6d1/ad4/6d1ad42a2c68788a504632f58d3ab1c982e16742/0b6b528de24dc38b312801853e639b91fbf40b21/README.yaml index 243c57427f..9902b4f170 100644 --- a/Simulations/6d1/ad4/6d1ad42a2c68788a504632f58d3ab1c982e16742/0b6b528de24dc38b312801853e639b91fbf40b21/README.yaml +++ b/Simulations/6d1/ad4/6d1ad42a2c68788a504632f58d3ab1c982e16742/0b6b528de24dc38b312801853e639b91fbf40b21/README.yaml @@ -50,9 +50,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/5 ID: 667 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (80:20) bilayer at 298.15 K (Lipid17, GROMACS 2021, 1001 ns) [NMRlipids simulation 667] + name: Molecular dynamics trajectory of a POPC/CHOL (80:20) bilayer at 298.15 K (Lipid17, + GROMACS 2021, 1001 ns) [NMRlipids simulation 667] alternateName: Lipid17_POPC_CHOL20_L - description: Molecular dynamics trajectory of a lipid bilayer of 1024 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 80 mol%) and 256 CHOL (cholesterol, 20 mol%) at 298.15 K. Simulated with Lipid17 in GROMACS 2021 for 1001 ns (348160 atoms). Deposited as NMRlipids Databank simulation 667 and available from https://doi.org/10.5281/zenodo.6992065. + description: Molecular dynamics trajectory of a lipid bilayer of 1024 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 80 mol%) and 256 CHOL (cholesterol, 20 mol%) at 298.15 K. Simulated with Lipid17 + in GROMACS 2021 for 1001 ns (348160 atoms). Deposited as NMRlipids Databank simulation + 667 and available from https://doi.org/10.5281/zenodo.6992065. sameAs: https://doi.org/10.5281/zenodo.6992065 datePublished: '2022-08-15' license: diff --git a/Simulations/6d2/5c5/6d25c53d444cee6ef6230a2b1db458398b369113/bbe038623632bc08db58561e71183052d5c47c02/README.yaml b/Simulations/6d2/5c5/6d25c53d444cee6ef6230a2b1db458398b369113/bbe038623632bc08db58561e71183052d5c47c02/README.yaml index f66374d647..4d03e60f7d 100644 --- a/Simulations/6d2/5c5/6d25c53d444cee6ef6230a2b1db458398b369113/bbe038623632bc08db58561e71183052d5c47c02/README.yaml +++ b/Simulations/6d2/5c5/6d25c53d444cee6ef6230a2b1db458398b369113/bbe038623632bc08db58561e71183052d5c47c02/README.yaml @@ -49,9 +49,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 17 bioschema_properties: - name: Molecular dynamics trajectory of a POPE/CLA/SOD (83:8:8) bilayer at 310 K (CHARMM36 and CHARMM TIP3P, GROMACS 5.1.2, 100 ns) [NMRlipids simulation 17] + name: Molecular dynamics trajectory of a POPE/CLA/SOD (83:8:8) bilayer at 310 K + (CHARMM36 and CHARMM TIP3P, GROMACS 5.1.2, 100 ns) [NMRlipids simulation 17] alternateName: 500POPE_25000SOL_50SOD_50CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 500 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 83 mol%), 50 CLA (8 mol%) and 50 SOD (8 mol%) at 310 K. Simulated with CHARMM36 and CHARMM TIP3P in GROMACS 5.1.2 for 100 ns (137600 atoms). Deposited as NMRlipids Databank simulation 17 and available from https://doi.org/10.5281/zenodo.2577454. + description: Molecular dynamics trajectory of a lipid bilayer of 500 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, + 83 mol%), 50 CLA (8 mol%) and 50 SOD (8 mol%) at 310 K. Simulated with CHARMM36 + and CHARMM TIP3P in GROMACS 5.1.2 for 100 ns (137600 atoms). Deposited as NMRlipids + Databank simulation 17 and available from https://doi.org/10.5281/zenodo.2577454. sameAs: https://doi.org/10.5281/zenodo.2577454 datePublished: '2019-02-26' license: diff --git a/Simulations/6d5/0e1/6d50e1333843d35d30bc8201a934539cae595d72/e5f6be84c833130b90c70d7fc612d0f85fcd8243/README.yaml b/Simulations/6d5/0e1/6d50e1333843d35d30bc8201a934539cae595d72/e5f6be84c833130b90c70d7fc612d0f85fcd8243/README.yaml index a741be1f17..d0e6c44268 100644 --- a/Simulations/6d5/0e1/6d50e1333843d35d30bc8201a934539cae595d72/e5f6be84c833130b90c70d7fc612d0f85fcd8243/README.yaml +++ b/Simulations/6d5/0e1/6d50e1333843d35d30bc8201a934539cae595d72/e5f6be84c833130b90c70d7fc612d0f85fcd8243/README.yaml @@ -51,9 +51,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/8 ID: 668 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (62:38) bilayer at 298.15 K (Slipids, GROMACS 2021, 1001 ns) [NMRlipids simulation 668] + name: Molecular dynamics trajectory of a POPC/CHOL (62:38) bilayer at 298.15 K (Slipids, + GROMACS 2021, 1001 ns) [NMRlipids simulation 668] alternateName: Slipids_POPC_CHOL38_M - description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 62 mol%) and 160 CHOL (cholesterol, 38 mol%) at 298.15 K. Simulated with Slipids in GROMACS 2021 for 1001 ns (108544 atoms). Deposited as NMRlipids Databank simulation 668 and available from https://doi.org/10.5281/zenodo.7022749. + description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 62 mol%) and 160 CHOL (cholesterol, 38 mol%) at 298.15 K. Simulated with Slipids + in GROMACS 2021 for 1001 ns (108544 atoms). Deposited as NMRlipids Databank simulation + 668 and available from https://doi.org/10.5281/zenodo.7022749. sameAs: https://doi.org/10.5281/zenodo.7022749 datePublished: '2022-08-23' license: diff --git a/Simulations/6d5/131/6d5131733214a5cdb69b1fa19d5e18a4b6694320/fac5ed76c777849ada7cde50ca64a6e06f0af9bc/README.yaml b/Simulations/6d5/131/6d5131733214a5cdb69b1fa19d5e18a4b6694320/fac5ed76c777849ada7cde50ca64a6e06f0af9bc/README.yaml index 7d5d10b8a7..9e4303ee6d 100644 --- a/Simulations/6d5/131/6d5131733214a5cdb69b1fa19d5e18a4b6694320/fac5ed76c777849ada7cde50ca64a6e06f0af9bc/README.yaml +++ b/Simulations/6d5/131/6d5131733214a5cdb69b1fa19d5e18a4b6694320/fac5ed76c777849ada7cde50ca64a6e06f0af9bc/README.yaml @@ -41,9 +41,12 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 361 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 303 K (CHARMM36, GROMACS 5.0.6, 500 ns) [NMRlipids simulation 361] + name: Molecular dynamics trajectory of a POPC bilayer at 303 K (CHARMM36, GROMACS + 5.0.6, 500 ns) [NMRlipids simulation 361] alternateName: 128POPC_5120SOL_10A-switch_v3 - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 303 K. Simulated with CHARMM36 in GROMACS 5.0.6 for 500 ns (32512 atoms). Deposited as NMRlipids Databank simulation 361 and available from https://doi.org/10.5281/zenodo.164206. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 303 K. Simulated with CHARMM36 in GROMACS 5.0.6 for 500 ns (32512 atoms). Deposited + as NMRlipids Databank simulation 361 and available from https://doi.org/10.5281/zenodo.164206. sameAs: https://doi.org/10.5281/zenodo.164206 datePublished: '2016-11-01' license: diff --git a/Simulations/6d7/4be/6d74bef991c67636ec4fe95680d3fffd418b64c6/77236938ba0b134b21fa55dfbfdbd8fbe0bde8d6/README.yaml b/Simulations/6d7/4be/6d74bef991c67636ec4fe95680d3fffd418b64c6/77236938ba0b134b21fa55dfbfdbd8fbe0bde8d6/README.yaml index eaf2311c8c..52f436d617 100644 --- a/Simulations/6d7/4be/6d74bef991c67636ec4fe95680d3fffd418b64c6/77236938ba0b134b21fa55dfbfdbd8fbe0bde8d6/README.yaml +++ b/Simulations/6d7/4be/6d74bef991c67636ec4fe95680d3fffd418b64c6/77236938ba0b134b21fa55dfbfdbd8fbe0bde8d6/README.yaml @@ -42,9 +42,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 669 bioschema_properties: - name: Molecular dynamics trajectory of a SOPC bilayer at 298.15 K (CHARMM36, GROMACS 2021, 1001 ns) [NMRlipids simulation 669] + name: Molecular dynamics trajectory of a SOPC bilayer at 298.15 K (CHARMM36, GROMACS + 2021, 1001 ns) [NMRlipids simulation 669] alternateName: SOPC_S - description: Molecular dynamics trajectory of a lipid bilayer of 64 SOPC (1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 298.15 K. Simulated with CHARMM36 in GROMACS 2021 for 1001 ns (18560 atoms). Deposited as NMRlipids Databank simulation 669 and available from https://doi.org/10.5281/zenodo.7103807. + description: Molecular dynamics trajectory of a lipid bilayer of 64 SOPC (1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 298.15 K. Simulated with CHARMM36 in GROMACS 2021 for 1001 ns (18560 atoms). + Deposited as NMRlipids Databank simulation 669 and available from https://doi.org/10.5281/zenodo.7103807. sameAs: https://doi.org/10.5281/zenodo.7103807 datePublished: '2022-09-22' license: diff --git a/Simulations/6d9/ea1/6d9ea166a012ce72b5552c6cb9589033d9fd3edf/6d9ea166a012ce72b5552c6cb9589033d9fd3edf/README.yaml b/Simulations/6d9/ea1/6d9ea166a012ce72b5552c6cb9589033d9fd3edf/6d9ea166a012ce72b5552c6cb9589033d9fd3edf/README.yaml index 821b13e15c..cad148c311 100644 --- a/Simulations/6d9/ea1/6d9ea166a012ce72b5552c6cb9589033d9fd3edf/6d9ea166a012ce72b5552c6cb9589033d9fd3edf/README.yaml +++ b/Simulations/6d9/ea1/6d9ea166a012ce72b5552c6cb9589033d9fd3edf/6d9ea166a012ce72b5552c6cb9589033d9fd3edf/README.yaml @@ -48,9 +48,13 @@ EXPERIMENT: TOCL: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a POT/TOCL/CLA (65:30:5) bilayer at 303 K (Charmm36, NAMD, 0 ns) [NMRlipids simulation 766] + name: Molecular dynamics trajectory of a POT/TOCL/CLA (65:30:5) bilayer at 303 K + (Charmm36, NAMD, 0 ns) [NMRlipids simulation 766] alternateName: TOCL NAMD - description: Molecular dynamics trajectory of a lipid bilayer of 215 POT (65 mol%), 100 TOCL (1’,3’-Bis[1,2-dioleoyl-sn-glycero-3-phospho]-glycerol, 30 mol%) and 15 CLA (5 mol%) at 303 K. Simulated with Charmm36 in NAMD for 0 ns (43030 atoms). Deposited as NMRlipids Databank simulation 766 and available from https://doi.org/10.5281/zenodo.8341624. + description: Molecular dynamics trajectory of a lipid bilayer of 215 POT (65 mol%), + 100 TOCL (1’,3’-Bis[1,2-dioleoyl-sn-glycero-3-phospho]-glycerol, 30 mol%) and + 15 CLA (5 mol%) at 303 K. Simulated with Charmm36 in NAMD for 0 ns (43030 atoms). + Deposited as NMRlipids Databank simulation 766 and available from https://doi.org/10.5281/zenodo.8341624. sameAs: https://doi.org/10.5281/zenodo.8341624 datePublished: '2023-09-13' license: diff --git a/Simulations/6df/e30/6dfe305837741f64feb89bba6ef9ae287cc69f03/5d840adb19c0153ec71e54f1dc918259bbcc6e6f/README.yaml b/Simulations/6df/e30/6dfe305837741f64feb89bba6ef9ae287cc69f03/5d840adb19c0153ec71e54f1dc918259bbcc6e6f/README.yaml index 61c7079ee1..0f953ca2e3 100644 --- a/Simulations/6df/e30/6dfe305837741f64feb89bba6ef9ae287cc69f03/5d840adb19c0153ec71e54f1dc918259bbcc6e6f/README.yaml +++ b/Simulations/6df/e30/6dfe305837741f64feb89bba6ef9ae287cc69f03/5d840adb19c0153ec71e54f1dc918259bbcc6e6f/README.yaml @@ -57,9 +57,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 440 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL/CHOL (43:31:16:11) bilayer at 310 K (Slipids with ECC-scaled ions (Kohagen), GROMACS 4.6, 600 ns) [NMRlipids simulation 440] + name: Molecular dynamics trajectory of a POPC/CLA/CAL/CHOL (43:31:16:11) bilayer + at 310 K (Slipids with ECC-scaled ions (Kohagen), GROMACS 4.6, 600 ns) [NMRlipids + simulation 440] alternateName: 50CHOL_200POPC_9000SOL_73CAL_146CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 43 mol%), 146 CLA (31 mol%), 73 CAL (16 mol%) and 50 CHOL (cholesterol, 11 mol%) at 310 K. Simulated with Slipids with ECC-scaled ions (Kohagen) in GROMACS 4.6 for 600 ns (57719 atoms). Deposited as NMRlipids Databank simulation 440 and available from https://doi.org/10.5281/zenodo.259354. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 43 mol%), 146 CLA (31 mol%), 73 CAL (16 mol%) and 50 CHOL (cholesterol, 11 mol%) + at 310 K. Simulated with Slipids with ECC-scaled ions (Kohagen) in GROMACS 4.6 + for 600 ns (57719 atoms). Deposited as NMRlipids Databank simulation 440 and available + from https://doi.org/10.5281/zenodo.259354. sameAs: https://doi.org/10.5281/zenodo.259354 datePublished: '2017-01-24' license: @@ -149,7 +155,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.259354 identifier: 10.5281/zenodo.259354 url: https://doi.org/10.5281/zenodo.259354 - name: Popc With Varying Amounts Of Cholesterol, 450 Mm Of Cacl_2. Slipids With Ecc-Scaled Ions + name: Popc With Varying Amounts Of Cholesterol, 450 Mm Of Cacl_2. Slipids With + Ecc-Scaled Ions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/6e0/4f3/6e04f3df4afc7b343445181dbf119a46b106fcb6/c08207cc0b28981f61fd8666533f6cdb505670ab/README.yaml b/Simulations/6e0/4f3/6e04f3df4afc7b343445181dbf119a46b106fcb6/c08207cc0b28981f61fd8666533f6cdb505670ab/README.yaml index ad58884e93..51052f5f85 100644 --- a/Simulations/6e0/4f3/6e04f3df4afc7b343445181dbf119a46b106fcb6/c08207cc0b28981f61fd8666533f6cdb505670ab/README.yaml +++ b/Simulations/6e0/4f3/6e04f3df4afc7b343445181dbf119a46b106fcb6/c08207cc0b28981f61fd8666533f6cdb505670ab/README.yaml @@ -55,9 +55,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 499 bioschema_properties: - name: Molecular dynamics trajectory of a CLA/POPC/CAL (43:35:22) bilayer at 313 K (ECC-lipids, GROMACS 5.1.4, 300 ns) [NMRlipids simulation 499] + name: Molecular dynamics trajectory of a CLA/POPC/CAL (43:35:22) bilayer at 313 + K (ECC-lipids, GROMACS 5.1.4, 300 ns) [NMRlipids simulation 499] alternateName: 128POPC_6232SOL_80CAL_160CLA_313K - description: Molecular dynamics trajectory of a lipid bilayer of 160 CLA (43 mol%), 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 35 mol%) and 80 CAL (22 mol%) at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 300 ns (36088 atoms). Deposited as NMRlipids Databank simulation 499 and available from https://doi.org/10.5281/zenodo.3335503. + description: Molecular dynamics trajectory of a lipid bilayer of 160 CLA (43 mol%), + 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 35 mol%) and 80 CAL + (22 mol%) at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 300 ns (36088 + atoms). Deposited as NMRlipids Databank simulation 499 and available from https://doi.org/10.5281/zenodo.3335503. sameAs: https://doi.org/10.5281/zenodo.3335503 datePublished: '2017-12-19' license: @@ -149,7 +153,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3335503 identifier: 10.5281/zenodo.3335503 url: https://doi.org/10.5281/zenodo.3335503 - name: Simulations of POPC lipid bilayer in water solution at various NaCl, KCl and CaCl2 concentrations using ECC-POPC force field + name: Simulations of POPC lipid bilayer in water solution at various NaCl, KCl + and CaCl2 concentrations using ECC-POPC force field publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/6e1/a5a/6e1a5ab968c2094bba1153cf8b30295accc56ca9/957cd6c5afe1348a1e92b5bb499bf2806d52f3ad/README.yaml b/Simulations/6e1/a5a/6e1a5ab968c2094bba1153cf8b30295accc56ca9/957cd6c5afe1348a1e92b5bb499bf2806d52f3ad/README.yaml index 9d869400b0..f9b184a54c 100644 --- a/Simulations/6e1/a5a/6e1a5ab968c2094bba1153cf8b30295accc56ca9/957cd6c5afe1348a1e92b5bb499bf2806d52f3ad/README.yaml +++ b/Simulations/6e1/a5a/6e1a5ab968c2094bba1153cf8b30295accc56ca9/957cd6c5afe1348a1e92b5bb499bf2806d52f3ad/README.yaml @@ -51,9 +51,13 @@ EXPERIMENT: CHOL: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a DOPC/CHOL (80:20) bilayer at 333.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 640] + name: Molecular dynamics trajectory of a DOPC/CHOL (80:20) bilayer at 333.15 K (CHARMM36, + GROMACS, 1001 ns) [NMRlipids simulation 640] alternateName: 1024DOPC_256CHOL_64000SOL_333K - description: Molecular dynamics trajectory of a lipid bilayer of 1024 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, 80 mol%) and 256 CHOL (cholesterol, 20 mol%) at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (352256 atoms). Deposited as NMRlipids Databank simulation 640 and available from https://doi.org/10.5281/zenodo.6943929. + description: Molecular dynamics trajectory of a lipid bilayer of 1024 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, + 80 mol%) and 256 CHOL (cholesterol, 20 mol%) at 333.15 K. Simulated with CHARMM36 + in GROMACS for 1001 ns (352256 atoms). Deposited as NMRlipids Databank simulation + 640 and available from https://doi.org/10.5281/zenodo.6943929. sameAs: https://doi.org/10.5281/zenodo.6943929 datePublished: '2022-07-30' license: diff --git a/Simulations/6e2/49f/6e249f03fc424603a0940513308cd5509e8562bd/6b93e7470d0062cef54e7e1abb7286774fc68d91/README.yaml b/Simulations/6e2/49f/6e249f03fc424603a0940513308cd5509e8562bd/6b93e7470d0062cef54e7e1abb7286774fc68d91/README.yaml index 18631fde03..949f9a4036 100644 --- a/Simulations/6e2/49f/6e249f03fc424603a0940513308cd5509e8562bd/6b93e7470d0062cef54e7e1abb7286774fc68d91/README.yaml +++ b/Simulations/6e2/49f/6e249f03fc424603a0940513308cd5509e8562bd/6b93e7470d0062cef54e7e1abb7286774fc68d91/README.yaml @@ -47,9 +47,12 @@ EXPERIMENT: FORMFACTOR: - 10.1021/jp511159q/1 bioschema_properties: - name: Molecular dynamics trajectory of a POPE bilayer at 310 K (OPLS-aa, GROMACS, 500 ns) [NMRlipids simulation 882] + name: Molecular dynamics trajectory of a POPE bilayer at 310 K (OPLS-aa, GROMACS, + 500 ns) [NMRlipids simulation 882] alternateName: Bilayer - description: Molecular dynamics trajectory of a lipid bilayer of 144 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) at 310 K. Simulated with OPLS-aa in GROMACS for 500 ns (35280 atoms). Deposited as NMRlipids Databank simulation 882 and available from https://doi.org/10.5281/zenodo.3571071. + description: Molecular dynamics trajectory of a lipid bilayer of 144 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) + at 310 K. Simulated with OPLS-aa in GROMACS for 500 ns (35280 atoms). Deposited + as NMRlipids Databank simulation 882 and available from https://doi.org/10.5281/zenodo.3571071. sameAs: https://doi.org/10.5281/zenodo.3571071 datePublished: '2019-12-11' license: diff --git a/Simulations/6e5/059/6e50598ebc47c6e57f6d242896be41b8a18de9a6/1c4ab02a568cca02b0eedbdc6c52ea136c2f3c40/README.yaml b/Simulations/6e5/059/6e50598ebc47c6e57f6d242896be41b8a18de9a6/1c4ab02a568cca02b0eedbdc6c52ea136c2f3c40/README.yaml index 8257cd0dd7..ad1ee3e64a 100644 --- a/Simulations/6e5/059/6e50598ebc47c6e57f6d242896be41b8a18de9a6/1c4ab02a568cca02b0eedbdc6c52ea136c2f3c40/README.yaml +++ b/Simulations/6e5/059/6e50598ebc47c6e57f6d242896be41b8a18de9a6/1c4ab02a568cca02b0eedbdc6c52ea136c2f3c40/README.yaml @@ -52,9 +52,14 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 226 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPG/POT (33:33:33) bilayer at 298 K (CHARMM36, GROMACS, 200 ns) [NMRlipids simulation 226] + name: Molecular dynamics trajectory of a POPC/POPG/POT (33:33:33) bilayer at 298 + K (CHARMM36, GROMACS, 200 ns) [NMRlipids simulation 226] alternateName: 250POPC_250POPG_250POT_298K_119974Atoms - description: Molecular dynamics trajectory of a lipid bilayer of 250 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 33 mol%), 250 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 33 mol%) and 250 POT (33 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for 200 ns (119974 atoms). Deposited as NMRlipids Databank simulation 226 and available from https://doi.org/10.5281/zenodo.3483787. + description: Molecular dynamics trajectory of a lipid bilayer of 250 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 33 mol%), 250 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 33 mol%) + and 250 POT (33 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for 200 ns + (119974 atoms). Deposited as NMRlipids Databank simulation 226 and available from + https://doi.org/10.5281/zenodo.3483787. sameAs: https://doi.org/10.5281/zenodo.3483787 datePublished: '2019-10-12' license: diff --git a/Simulations/6e8/031/6e803117ac69d06705e1f024f63ae7e324a0677b/788e5d78db0bd8aafdf3f1d1c0acc33cd7ad0a71/README.yaml b/Simulations/6e8/031/6e803117ac69d06705e1f024f63ae7e324a0677b/788e5d78db0bd8aafdf3f1d1c0acc33cd7ad0a71/README.yaml index a687534255..04a6c55621 100644 --- a/Simulations/6e8/031/6e803117ac69d06705e1f024f63ae7e324a0677b/788e5d78db0bd8aafdf3f1d1c0acc33cd7ad0a71/README.yaml +++ b/Simulations/6e8/031/6e803117ac69d06705e1f024f63ae7e324a0677b/788e5d78db0bd8aafdf3f1d1c0acc33cd7ad0a71/README.yaml @@ -51,9 +51,13 @@ DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 610 AUTHORS_CONTACT: Santuz, Hubert bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (81:19) bilayer at 303 K (CHARMM36, GROMACS, 200 ns) [NMRlipids simulation 610] + name: Molecular dynamics trajectory of a POPC/CHOL (81:19) bilayer at 303 K (CHARMM36, + GROMACS, 200 ns) [NMRlipids simulation 610] alternateName: POPC20%chol_T303K - description: Molecular dynamics trajectory of a lipid bilayer of 100 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 81 mol%) and 24 CHOL (cholesterol, 19 mol%) at 303 K. Simulated with CHARMM36 in GROMACS for 200 ns (30056 atoms). Deposited as NMRlipids Databank simulation 610 and available from https://doi.org/10.5281/zenodo.14067. + description: Molecular dynamics trajectory of a lipid bilayer of 100 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 81 mol%) and 24 CHOL (cholesterol, 19 mol%) at 303 K. Simulated with CHARMM36 + in GROMACS for 200 ns (30056 atoms). Deposited as NMRlipids Databank simulation + 610 and available from https://doi.org/10.5281/zenodo.14067. sameAs: https://doi.org/10.5281/zenodo.14067 datePublished: '2015-01-19' license: diff --git a/Simulations/6e9/136/6e91368ecf1fde6a9d5fcdbe16690e3bf74fd4fe/1c39a498bfc3d7a4dbdb25ebbf2bc57ade06531d/README.yaml b/Simulations/6e9/136/6e91368ecf1fde6a9d5fcdbe16690e3bf74fd4fe/1c39a498bfc3d7a4dbdb25ebbf2bc57ade06531d/README.yaml index 0d452331d3..0801a85bc8 100644 --- a/Simulations/6e9/136/6e91368ecf1fde6a9d5fcdbe16690e3bf74fd4fe/1c39a498bfc3d7a4dbdb25ebbf2bc57ade06531d/README.yaml +++ b/Simulations/6e9/136/6e91368ecf1fde6a9d5fcdbe16690e3bf74fd4fe/1c39a498bfc3d7a4dbdb25ebbf2bc57ade06531d/README.yaml @@ -59,9 +59,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 314 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/SOD/CLA/POPS (37:31:24:7) bilayer at 298 K (Lipid17 and ff99 ions, GROMACS 2018.0, 652 ns) [NMRlipids simulation 314] + name: Molecular dynamics trajectory of a POPC/SOD/CLA/POPS (37:31:24:7) bilayer + at 298 K (Lipid17 and ff99 ions, GROMACS 2018.0, 652 ns) [NMRlipids simulation + 314] alternateName: 12POPS_60POPC_3483SOL_51SOD_39CLA_298K - description: Molecular dynamics trajectory of a lipid bilayer of 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 37 mol%), 51 SOD (31 mol%), 39 CLA (24 mol%) and 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 7 mol%) at 298 K. Simulated with Lipid17 and ff99 ions in GROMACS 2018.0 for 652 ns (20103 atoms). Deposited as NMRlipids Databank simulation 314 and available from https://doi.org/10.5281/zenodo.1487906. + description: Molecular dynamics trajectory of a lipid bilayer of 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 37 mol%), 51 SOD (31 mol%), 39 CLA (24 mol%) and 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, + 7 mol%) at 298 K. Simulated with Lipid17 and ff99 ions in GROMACS 2018.0 for 652 + ns (20103 atoms). Deposited as NMRlipids Databank simulation 314 and available + from https://doi.org/10.5281/zenodo.1487906. sameAs: https://doi.org/10.5281/zenodo.1487906 datePublished: '2018-11-14' license: @@ -153,7 +159,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1487906 identifier: 10.5281/zenodo.1487906 url: https://doi.org/10.5281/zenodo.1487906 - name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS with the lipid17 force field and ff99 ions + name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS + with the lipid17 force field and ff99 ions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/6e9/72a/6e972a7fd3a1a9b77dcaf509b8320a27de212b13/7d5c9fde9b9d85c2ad7bbcffaee4c5141de13566/README.yaml b/Simulations/6e9/72a/6e972a7fd3a1a9b77dcaf509b8320a27de212b13/7d5c9fde9b9d85c2ad7bbcffaee4c5141de13566/README.yaml index 1f937718a6..b21a61a907 100644 --- a/Simulations/6e9/72a/6e972a7fd3a1a9b77dcaf509b8320a27de212b13/7d5c9fde9b9d85c2ad7bbcffaee4c5141de13566/README.yaml +++ b/Simulations/6e9/72a/6e972a7fd3a1a9b77dcaf509b8320a27de212b13/7d5c9fde9b9d85c2ad7bbcffaee4c5141de13566/README.yaml @@ -63,9 +63,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 313 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPS/SOD/CLA/CAL (61:12:12:10:5) bilayer at 298 K (Lipid17 and Dang ions, GROMACS 2018.0, 1000 ns) [NMRlipids simulation 313] + name: Molecular dynamics trajectory of a POPC/POPS/SOD/CLA/CAL (61:12:12:10:5) bilayer + at 298 K (Lipid17 and Dang ions, GROMACS 2018.0, 1000 ns) [NMRlipids simulation + 313] alternateName: 60POPC_12POPS_3561SOL_5CAL_10CLA_12SOD_298K - description: Molecular dynamics trajectory of a lipid bilayer of 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 61 mol%), 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 12 mol%), 12 SOD (12 mol%), 10 CLA (10 mol%) and 5 CAL (5 mol%) at 298 K. Simulated with Lipid17 and Dang ions in GROMACS 2018.0 for 1000 ns (20274 atoms). Deposited as NMRlipids Databank simulation 313 and available from https://doi.org/10.5281/zenodo.1487761. + description: Molecular dynamics trajectory of a lipid bilayer of 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 61 mol%), 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 12 mol%), + 12 SOD (12 mol%), 10 CLA (10 mol%) and 5 CAL (5 mol%) at 298 K. Simulated with + Lipid17 and Dang ions in GROMACS 2018.0 for 1000 ns (20274 atoms). Deposited as + NMRlipids Databank simulation 313 and available from https://doi.org/10.5281/zenodo.1487761. sameAs: https://doi.org/10.5281/zenodo.1487761 datePublished: '2018-11-14' license: @@ -158,7 +164,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1487761 identifier: 10.5281/zenodo.1487761 url: https://doi.org/10.5281/zenodo.1487761 - name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS with the lipid17 force field, only counterions, and CaCl2 concentrations + name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS + with the lipid17 force field, only counterions, and CaCl2 concentrations publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/6ea/fe9/6eafe9c6c56daa36f0af14e64837cdc34719da24/68f5668737c881e7a47ad99f27270cdf36c78477/README.yaml b/Simulations/6ea/fe9/6eafe9c6c56daa36f0af14e64837cdc34719da24/68f5668737c881e7a47ad99f27270cdf36c78477/README.yaml index 684c31bd9b..47a244c4d8 100644 --- a/Simulations/6ea/fe9/6eafe9c6c56daa36f0af14e64837cdc34719da24/68f5668737c881e7a47ad99f27270cdf36c78477/README.yaml +++ b/Simulations/6ea/fe9/6eafe9c6c56daa36f0af14e64837cdc34719da24/68f5668737c881e7a47ad99f27270cdf36c78477/README.yaml @@ -52,9 +52,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 485 bioschema_properties: - name: Molecular dynamics trajectory of a POPG/SOD/POPE (43:43:14) bilayer at 310 K (CHARMM36, GROMACS 2018.3, 100 ns) [NMRlipids simulation 485] + name: Molecular dynamics trajectory of a POPG/SOD/POPE (43:43:14) bilayer at 310 + K (CHARMM36, GROMACS 2018.3, 100 ns) [NMRlipids simulation 485] alternateName: 374POPG_126POPE_25000SOL_374SOD_310K - description: Molecular dynamics trajectory of a lipid bilayer of 374 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 43 mol%), 374 SOD (43 mol%) and 126 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 14 mol%) at 310 K. Simulated with CHARMM36 in GROMACS 2018.3 for 100 ns (138622 atoms). Deposited as NMRlipids Databank simulation 485 and available from https://doi.org/10.5281/zenodo.3250127. + description: Molecular dynamics trajectory of a lipid bilayer of 374 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, + 43 mol%), 374 SOD (43 mol%) and 126 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, + 14 mol%) at 310 K. Simulated with CHARMM36 in GROMACS 2018.3 for 100 ns (138622 + atoms). Deposited as NMRlipids Databank simulation 485 and available from https://doi.org/10.5281/zenodo.3250127. sameAs: https://doi.org/10.5281/zenodo.3250127 datePublished: '2019-06-19' license: diff --git a/Simulations/6eb/dbf/6ebdbfc108ce1205a1f50039ea1b7129cad1534a/45c63a6b3ce74d4d0e5c03656cae0fc68faeceb4/README.yaml b/Simulations/6eb/dbf/6ebdbfc108ce1205a1f50039ea1b7129cad1534a/45c63a6b3ce74d4d0e5c03656cae0fc68faeceb4/README.yaml index cc94e3bc6f..0589c8f4c3 100644 --- a/Simulations/6eb/dbf/6ebdbfc108ce1205a1f50039ea1b7129cad1534a/45c63a6b3ce74d4d0e5c03656cae0fc68faeceb4/README.yaml +++ b/Simulations/6eb/dbf/6ebdbfc108ce1205a1f50039ea1b7129cad1534a/45c63a6b3ce74d4d0e5c03656cae0fc68faeceb4/README.yaml @@ -49,9 +49,13 @@ EXPERIMENT: - 10.1016/j.bbamem.2011.07.022/4 ID: 472 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC bilayer at 323 K (OPLSAA-compatible Berger-DPPC-06, GROMACS 5.1-beta, 120 ns) [NMRlipids simulation 472] + name: Molecular dynamics trajectory of a DPPC bilayer at 323 K (OPLSAA-compatible + Berger-DPPC-06, GROMACS 5.1-beta, 120 ns) [NMRlipids simulation 472] alternateName: 72DPPC_2880SOL_323K_Berger - description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) at 323 K. Simulated with OPLSAA-compatible Berger-DPPC-06 in GROMACS 5.1-beta for 120 ns (12240 atoms). Deposited as NMRlipids Databank simulation 472 and available from https://doi.org/10.5281/zenodo.17237. + description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) + at 323 K. Simulated with OPLSAA-compatible Berger-DPPC-06 in GROMACS 5.1-beta + for 120 ns (12240 atoms). Deposited as NMRlipids Databank simulation 472 and available + from https://doi.org/10.5281/zenodo.17237. sameAs: https://doi.org/10.5281/zenodo.17237 datePublished: '2015-04-29' license: diff --git a/Simulations/6f0/eb4/6f0eb4af02a08af3f70ccc52a3a5ee1e6852da6d/386190dbaa6fe66b1668c0a4fc291a212ea8397d/README.yaml b/Simulations/6f0/eb4/6f0eb4af02a08af3f70ccc52a3a5ee1e6852da6d/386190dbaa6fe66b1668c0a4fc291a212ea8397d/README.yaml index e7b2f50fe7..b01f6aad49 100644 --- a/Simulations/6f0/eb4/6f0eb4af02a08af3f70ccc52a3a5ee1e6852da6d/386190dbaa6fe66b1668c0a4fc291a212ea8397d/README.yaml +++ b/Simulations/6f0/eb4/6f0eb4af02a08af3f70ccc52a3a5ee1e6852da6d/386190dbaa6fe66b1668c0a4fc291a212ea8397d/README.yaml @@ -53,9 +53,14 @@ EXPERIMENT: POPE: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a SOD/POPG/POPE/CLA (44:38:13:5) bilayer at 310 K (Slipids, GROMACS 5.1.2, 100 ns) [NMRlipids simulation 883] + name: Molecular dynamics trajectory of a SOD/POPG/POPE/CLA (44:38:13:5) bilayer + at 310 K (Slipids, GROMACS 5.1.2, 100 ns) [NMRlipids simulation 883] alternateName: POPG-POPE 3:1 Bilayer Simulation - description: Molecular dynamics trajectory of a lipid bilayer of 423 SOD (44 mol%), 374 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 38 mol%), 126 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 13 mol%) and 49 CLA (5 mol%) at 310 K. Simulated with Slipids in GROMACS 5.1.2 for 100 ns (138720 atoms). Deposited as NMRlipids Databank simulation 883 and available from https://doi.org/10.5281/zenodo.2579675. + description: Molecular dynamics trajectory of a lipid bilayer of 423 SOD (44 mol%), + 374 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 38 mol%), 126 POPE + (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 13 mol%) and 49 CLA (5 + mol%) at 310 K. Simulated with Slipids in GROMACS 5.1.2 for 100 ns (138720 atoms). + Deposited as NMRlipids Databank simulation 883 and available from https://doi.org/10.5281/zenodo.2579675. sameAs: https://doi.org/10.5281/zenodo.2579675 datePublished: '2019-02-28' license: @@ -148,7 +153,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.2579675 identifier: 10.5281/zenodo.2579675 url: https://doi.org/10.5281/zenodo.2579675 - name: SLIPID POPG-POPE 3:1 Bilayer Simulation (Last 100 ns, 150 mM NaCl, 310 K ) + name: SLIPID POPG-POPE 3:1 Bilayer Simulation (Last 100 ns, 150 mM NaCl, 310 K + ) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/6f1/985/6f1985d98f7208b300154ddee26c6db9e3c9f625/0f12a1455304c234e5673a42f68745a375ca5b84/README.yaml b/Simulations/6f1/985/6f1985d98f7208b300154ddee26c6db9e3c9f625/0f12a1455304c234e5673a42f68745a375ca5b84/README.yaml index d1625c7e54..f837d422c4 100644 --- a/Simulations/6f1/985/6f1985d98f7208b300154ddee26c6db9e3c9f625/0f12a1455304c234e5673a42f68745a375ca5b84/README.yaml +++ b/Simulations/6f1/985/6f1985d98f7208b300154ddee26c6db9e3c9f625/0f12a1455304c234e5673a42f68745a375ca5b84/README.yaml @@ -57,9 +57,14 @@ SOFTWARE: gromacs DIR_WRK: /usr/home/bort/Databank ID: 12 bioschema_properties: - name: Molecular dynamics trajectory of a DOPC/DLIPC/CHOL (46:44:10) bilayer at 310 K (CHARMM36, GROMACS, 1000 ns) [NMRlipids simulation 12] + name: Molecular dynamics trajectory of a DOPC/DLIPC/CHOL (46:44:10) bilayer at 310 + K (CHARMM36, GROMACS, 1000 ns) [NMRlipids simulation 12] alternateName: 28CHOL_130DOPC_125DLIPC_11320SOL_310K - description: Molecular dynamics trajectory of a lipid bilayer of 130 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, 46 mol%), 125 DLIPC (1,2-dilinoleoyl-sn-glycero-3-phosphocholine, 44 mol%) and 28 CHOL (cholesterol, 10 mol%) at 310 K. Simulated with CHARMM36 in GROMACS for 1000 ns (70722 atoms). Deposited as NMRlipids Databank simulation 12 and available from https://doi.org/10.5281/zenodo.2653723. + description: Molecular dynamics trajectory of a lipid bilayer of 130 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, + 46 mol%), 125 DLIPC (1,2-dilinoleoyl-sn-glycero-3-phosphocholine, 44 mol%) and + 28 CHOL (cholesterol, 10 mol%) at 310 K. Simulated with CHARMM36 in GROMACS for + 1000 ns (70722 atoms). Deposited as NMRlipids Databank simulation 12 and available + from https://doi.org/10.5281/zenodo.2653723. sameAs: https://doi.org/10.5281/zenodo.2653723 datePublished: '2019-04-29' license: @@ -150,7 +155,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.2653723 identifier: 10.5281/zenodo.2653723 url: https://doi.org/10.5281/zenodo.2653723 - name: Atomistic simulations of cholesterol in asymmetric lipid bilayers with varying degrees of lipid chain unsaturation + name: Atomistic simulations of cholesterol in asymmetric lipid bilayers with varying + degrees of lipid chain unsaturation publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/6f6/38a/6f638ad75234c64e89f8db0a1e400ef6bc3599b3/8045be2ac27431ebb3009c682317937b954da3f1/README.yaml b/Simulations/6f6/38a/6f638ad75234c64e89f8db0a1e400ef6bc3599b3/8045be2ac27431ebb3009c682317937b954da3f1/README.yaml index 9b2c504aa4..d6bd14f240 100644 --- a/Simulations/6f6/38a/6f638ad75234c64e89f8db0a1e400ef6bc3599b3/8045be2ac27431ebb3009c682317937b954da3f1/README.yaml +++ b/Simulations/6f6/38a/6f638ad75234c64e89f8db0a1e400ef6bc3599b3/8045be2ac27431ebb3009c682317937b954da3f1/README.yaml @@ -56,9 +56,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 395 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/CLA/SOD/CHOL (74:9:9:9) bilayer at 320 K (Slipids, GROMACS, 500 ns) [NMRlipids simulation 395] + name: Molecular dynamics trajectory of a DPPC/CLA/SOD/CHOL (74:9:9:9) bilayer at + 320 K (Slipids, GROMACS, 500 ns) [NMRlipids simulation 395] alternateName: 1032DPPC_120CHOL_46440SOL_124SOD_124CLA_320K - description: Molecular dynamics trajectory of a lipid bilayer of 1032 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 74 mol%), 124 CLA (9 mol%), 124 SOD (9 mol%) and 120 CHOL (cholesterol, 9 mol%) at 320 K. Simulated with Slipids in GROMACS for 500 ns (282608 atoms). Deposited as NMRlipids Databank simulation 395 and available from https://doi.org/10.5281/zenodo.3539263. + description: Molecular dynamics trajectory of a lipid bilayer of 1032 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 74 mol%), 124 CLA (9 mol%), 124 SOD (9 mol%) and 120 CHOL (cholesterol, 9 mol%) + at 320 K. Simulated with Slipids in GROMACS for 500 ns (282608 atoms). Deposited + as NMRlipids Databank simulation 395 and available from https://doi.org/10.5281/zenodo.3539263. sameAs: https://doi.org/10.5281/zenodo.3539263 datePublished: '2019-11-12' license: diff --git a/Simulations/702/d04/702d047ee14fb2c6b8ceb1666df45f0783272d8c/50161179ab704faeaf1644957545a77fe97a1063/README.yaml b/Simulations/702/d04/702d047ee14fb2c6b8ceb1666df45f0783272d8c/50161179ab704faeaf1644957545a77fe97a1063/README.yaml index 269894574a..a772de97a1 100644 --- a/Simulations/702/d04/702d047ee14fb2c6b8ceb1666df45f0783272d8c/50161179ab704faeaf1644957545a77fe97a1063/README.yaml +++ b/Simulations/702/d04/702d047ee14fb2c6b8ceb1666df45f0783272d8c/50161179ab704faeaf1644957545a77fe97a1063/README.yaml @@ -55,9 +55,13 @@ DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 51 AUTHORS_CONTACT: Ollila, O. H. Samuli bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/DHMDMAB (62:19:19) bilayer at 313 K (CHARMM36, GROMACS, 200 ns) [NMRlipids simulation 51] + name: Molecular dynamics trajectory of a POPC/CLA/DHMDMAB (62:19:19) bilayer at + 313 K (CHARMM36, GROMACS, 200 ns) [NMRlipids simulation 51] alternateName: POPC10%DHMDMAB_T313K - description: Molecular dynamics trajectory of a lipid bilayer of 100 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 62 mol%), 30 CLA (19 mol%) and 30 DHMDMAB (dihexadecyldimethylammonium, 19 mol%) at 313 K. Simulated with CHARMM36 in GROMACS for 200 ns (40538 atoms). Deposited as NMRlipids Databank simulation 51 and available from https://doi.org/10.5281/zenodo.1288297. + description: Molecular dynamics trajectory of a lipid bilayer of 100 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 62 mol%), 30 CLA (19 mol%) and 30 DHMDMAB (dihexadecyldimethylammonium, 19 mol%) + at 313 K. Simulated with CHARMM36 in GROMACS for 200 ns (40538 atoms). Deposited + as NMRlipids Databank simulation 51 and available from https://doi.org/10.5281/zenodo.1288297. sameAs: https://doi.org/10.5281/zenodo.1288297 datePublished: '2018-06-13' license: diff --git a/Simulations/708/bd6/708bd65822fac491c4dd8994bc312a81d3cfbbdb/4fad5e4406377929bbff830d0a015465a4322aa8/README.yaml b/Simulations/708/bd6/708bd65822fac491c4dd8994bc312a81d3cfbbdb/4fad5e4406377929bbff830d0a015465a4322aa8/README.yaml index 0d0158ccb2..a5faaf0d9a 100644 --- a/Simulations/708/bd6/708bd65822fac491c4dd8994bc312a81d3cfbbdb/4fad5e4406377929bbff830d0a015465a4322aa8/README.yaml +++ b/Simulations/708/bd6/708bd65822fac491c4dd8994bc312a81d3cfbbdb/4fad5e4406377929bbff830d0a015465a4322aa8/README.yaml @@ -55,9 +55,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 492 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPS/POT (33:33:33) bilayer at 298 K (Lipid17 and Dang ions, GROMACS 2018.0, 1000 ns) [NMRlipids simulation 492] + name: Molecular dynamics trajectory of a POPC/POPS/POT (33:33:33) bilayer at 298 + K (Lipid17 and Dang ions, GROMACS 2018.0, 1000 ns) [NMRlipids simulation 492] alternateName: 64POPC_64POPS_5253SOL_64POT_298K - description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 33 mol%), 64 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 33 mol%) and 64 POT (33 mol%) at 298 K. Simulated with Lipid17 and Dang ions in GROMACS 2018.0 for 1000 ns (32527 atoms). Deposited as NMRlipids Databank simulation 492 and available from https://doi.org/10.5281/zenodo.1487761. + description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 33 mol%), 64 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 33 mol%) + and 64 POT (33 mol%) at 298 K. Simulated with Lipid17 and Dang ions in GROMACS + 2018.0 for 1000 ns (32527 atoms). Deposited as NMRlipids Databank simulation 492 + and available from https://doi.org/10.5281/zenodo.1487761. sameAs: https://doi.org/10.5281/zenodo.1487761 datePublished: '2018-11-14' license: @@ -148,7 +153,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1487761 identifier: 10.5281/zenodo.1487761 url: https://doi.org/10.5281/zenodo.1487761 - name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS with the lipid17 force field, only counterions, and CaCl2 concentrations + name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS + with the lipid17 force field, only counterions, and CaCl2 concentrations publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/708/ca1/708ca1f2ad04cd4ce023aa6b0f0b10f1f0bea3ec/9eedba5b0a8dff69e5027cdbe529851b465f1139/README.yaml b/Simulations/708/ca1/708ca1f2ad04cd4ce023aa6b0f0b10f1f0bea3ec/9eedba5b0a8dff69e5027cdbe529851b465f1139/README.yaml index e9375146aa..e68cf9d006 100644 --- a/Simulations/708/ca1/708ca1f2ad04cd4ce023aa6b0f0b10f1f0bea3ec/9eedba5b0a8dff69e5027cdbe529851b465f1139/README.yaml +++ b/Simulations/708/ca1/708ca1f2ad04cd4ce023aa6b0f0b10f1f0bea3ec/9eedba5b0a8dff69e5027cdbe529851b465f1139/README.yaml @@ -44,9 +44,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 799 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 300 K (OPLS4, GROMACS Desmond XXXX-X, 400 ns) [NMRlipids simulation 799] + name: Molecular dynamics trajectory of a POPC bilayer at 300 K (OPLS4, GROMACS Desmond + XXXX-X, 400 ns) [NMRlipids simulation 799] alternateName: 200POPC_2000SOL_300K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 300 K. Simulated with OPLS4 in GROMACS Desmond XXXX-X for 400 ns (32800 atoms). Deposited as NMRlipids Databank simulation 799 and available from https://doi.org/10.5281/zenodo.10930798. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 300 K. Simulated with OPLS4 in GROMACS Desmond XXXX-X for 400 ns (32800 atoms). + Deposited as NMRlipids Databank simulation 799 and available from https://doi.org/10.5281/zenodo.10930798. sameAs: https://doi.org/10.5281/zenodo.10930798 datePublished: '2024-04-05' license: diff --git a/Simulations/710/317/710317be51c54051bda8fcc9f46709b5922b9c33/a94db18fc5aa0d86a13d16b5ed5dc677d19c3b57/README.yaml b/Simulations/710/317/710317be51c54051bda8fcc9f46709b5922b9c33/a94db18fc5aa0d86a13d16b5ed5dc677d19c3b57/README.yaml index 51eaa46034..1835e4ffea 100644 --- a/Simulations/710/317/710317be51c54051bda8fcc9f46709b5922b9c33/a94db18fc5aa0d86a13d16b5ed5dc677d19c3b57/README.yaml +++ b/Simulations/710/317/710317be51c54051bda8fcc9f46709b5922b9c33/a94db18fc5aa0d86a13d16b5ed5dc677d19c3b57/README.yaml @@ -52,9 +52,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 555 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPS/POT (71:14:14) bilayer at 298 K (CHARMM36, GROMACS, 200 ns) [NMRlipids simulation 555] + name: Molecular dynamics trajectory of a POPC/POPS/POT (71:14:14) bilayer at 298 + K (CHARMM36, GROMACS, 200 ns) [NMRlipids simulation 555] alternateName: 250POPC_50POPS_50POT_298K_73521Atoms - description: Molecular dynamics trajectory of a lipid bilayer of 250 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 71 mol%), 50 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 14 mol%) and 50 POT (14 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for 200 ns (73521 atoms). Deposited as NMRlipids Databank simulation 555 and available from https://doi.org/10.5281/zenodo.2542151. + description: Molecular dynamics trajectory of a lipid bilayer of 250 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 71 mol%), 50 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 14 mol%) + and 50 POT (14 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for 200 ns (73521 + atoms). Deposited as NMRlipids Databank simulation 555 and available from https://doi.org/10.5281/zenodo.2542151. sameAs: https://doi.org/10.5281/zenodo.2542151 datePublished: '2019-01-16' license: diff --git a/Simulations/714/514/714514b555844f65fb55c81107f55874f47f48bd/6031437b2f39fcf7f7626fb5168661c855adbd7f/README.yaml b/Simulations/714/514/714514b555844f65fb55c81107f55874f47f48bd/6031437b2f39fcf7f7626fb5168661c855adbd7f/README.yaml index e857b5f68b..1d9fa76d41 100644 --- a/Simulations/714/514/714514b555844f65fb55c81107f55874f47f48bd/6031437b2f39fcf7f7626fb5168661c855adbd7f/README.yaml +++ b/Simulations/714/514/714514b555844f65fb55c81107f55874f47f48bd/6031437b2f39fcf7f7626fb5168661c855adbd7f/README.yaml @@ -51,9 +51,15 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 83 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (48:35:17) bilayer at 310.15 K (CHARMM36 with incorrect multiplicity in dihedrals and ECC ions, GROMACS 5.0, 800 ns) [NMRlipids simulation 83] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (48:35:17) bilayer at 310.15 + K (CHARMM36 with incorrect multiplicity in dihedrals and ECC ions, GROMACS 5.0, + 800 ns) [NMRlipids simulation 83] alternateName: 200POPC_9000SOL_73CAL_146CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 48 mol%), 146 CLA (35 mol%) and 73 CAL (17 mol%) at 310.15 K. Simulated with CHARMM36 with incorrect multiplicity in dihedrals and ECC ions in GROMACS 5.0 for 800 ns (54019 atoms). Deposited as NMRlipids Databank simulation 83 and available from https://doi.org/10.5281/zenodo.259376. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 48 mol%), 146 CLA (35 mol%) and 73 CAL (17 mol%) at 310.15 K. Simulated with CHARMM36 + with incorrect multiplicity in dihedrals and ECC ions in GROMACS 5.0 for 800 ns + (54019 atoms). Deposited as NMRlipids Databank simulation 83 and available from + https://doi.org/10.5281/zenodo.259376. sameAs: https://doi.org/10.5281/zenodo.259376 datePublished: '2017-01-24' license: @@ -141,7 +147,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.259376 identifier: 10.5281/zenodo.259376 url: https://doi.org/10.5281/zenodo.259376 - name: Popc With Varying Amounts Of Cholesterol, 450 Mm Of Cacl_2. Charmm36 With Ecc-Scaled Ions + name: Popc With Varying Amounts Of Cholesterol, 450 Mm Of Cacl_2. Charmm36 With + Ecc-Scaled Ions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/715/726/715726bb53690ba703a42499cdcb3d3d75a3638d/9f2ead75cff9dd55b3b747d888f19451b5f7b18d/README.yaml b/Simulations/715/726/715726bb53690ba703a42499cdcb3d3d75a3638d/9f2ead75cff9dd55b3b747d888f19451b5f7b18d/README.yaml index 8eeaabdbde..2c09e1af4e 100644 --- a/Simulations/715/726/715726bb53690ba703a42499cdcb3d3d75a3638d/9f2ead75cff9dd55b3b747d888f19451b5f7b18d/README.yaml +++ b/Simulations/715/726/715726bb53690ba703a42499cdcb3d3d75a3638d/9f2ead75cff9dd55b3b747d888f19451b5f7b18d/README.yaml @@ -44,9 +44,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 328 bioschema_properties: - name: Molecular dynamics trajectory of a POPE bilayer at 313 K (GROMOS-CKP, GROMACS 5.0.6, 400 ns) [NMRlipids simulation 328] + name: Molecular dynamics trajectory of a POPE bilayer at 313 K (GROMOS-CKP, GROMACS + 5.0.6, 400 ns) [NMRlipids simulation 328] alternateName: 128POPE_3552SOL_313K_GROMOS-CKP_v1 - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) at 313 K. Simulated with GROMOS-CKP in GROMACS 5.0.6 for 400 ns (17312 atoms). Deposited as NMRlipids Databank simulation 328 and available from https://doi.org/10.5281/zenodo.1293932. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) + at 313 K. Simulated with GROMOS-CKP in GROMACS 5.0.6 for 400 ns (17312 atoms). + Deposited as NMRlipids Databank simulation 328 and available from https://doi.org/10.5281/zenodo.1293932. sameAs: https://doi.org/10.5281/zenodo.1293932 datePublished: '2018-06-20' license: diff --git a/Simulations/71a/122/71a122c0825c0aa8efa4b2ab6dbd0b3ceb6f4abe/7a4a14b92fc5cc472f87982f94dc715d2de7ab75/README.yaml b/Simulations/71a/122/71a122c0825c0aa8efa4b2ab6dbd0b3ceb6f4abe/7a4a14b92fc5cc472f87982f94dc715d2de7ab75/README.yaml index 189a403899..0e0f8fdab5 100644 --- a/Simulations/71a/122/71a122c0825c0aa8efa4b2ab6dbd0b3ceb6f4abe/7a4a14b92fc5cc472f87982f94dc715d2de7ab75/README.yaml +++ b/Simulations/71a/122/71a122c0825c0aa8efa4b2ab6dbd0b3ceb6f4abe/7a4a14b92fc5cc472f87982f94dc715d2de7ab75/README.yaml @@ -42,9 +42,12 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 623 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 310.15 K (CHARMM36, GROMACS 5.0, 500 ns) [NMRlipids simulation 623] + name: Molecular dynamics trajectory of a POPC bilayer at 310.15 K (CHARMM36, GROMACS + 5.0, 500 ns) [NMRlipids simulation 623] alternateName: 200POPC_9000SOL_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 310.15 K. Simulated with CHARMM36 in GROMACS 5.0 for 500 ns (53800 atoms). Deposited as NMRlipids Databank simulation 623 and available from https://doi.org/10.5281/zenodo.3237420. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 310.15 K. Simulated with CHARMM36 in GROMACS 5.0 for 500 ns (53800 atoms). + Deposited as NMRlipids Databank simulation 623 and available from https://doi.org/10.5281/zenodo.3237420. sameAs: https://doi.org/10.5281/zenodo.3237420 datePublished: '2016-10-09' license: @@ -131,7 +134,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3237420 identifier: 10.5281/zenodo.3237420 url: https://doi.org/10.5281/zenodo.3237420 - name: POPC with 0, 10, 20, and 30 mol-% of cholesterol at 310 K. Charmm36 force field. + name: POPC with 0, 10, 20, and 30 mol-% of cholesterol at 310 K. Charmm36 force + field. publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/71f/f4b/71ff4b2a46851e718c2572520e60ff442865d6ff/7d172d134eeeded0a74a8d3f27962d04e37d2b2e/README.yaml b/Simulations/71f/f4b/71ff4b2a46851e718c2572520e60ff442865d6ff/7d172d134eeeded0a74a8d3f27962d04e37d2b2e/README.yaml index 7ccd5ae27d..8b625635b5 100644 --- a/Simulations/71f/f4b/71ff4b2a46851e718c2572520e60ff442865d6ff/7d172d134eeeded0a74a8d3f27962d04e37d2b2e/README.yaml +++ b/Simulations/71f/f4b/71ff4b2a46851e718c2572520e60ff442865d6ff/7d172d134eeeded0a74a8d3f27962d04e37d2b2e/README.yaml @@ -52,9 +52,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 318 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (92:4:4) bilayer at 310 K (CHARMM36, GROMACS, 667 ns) [NMRlipids simulation 318] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (92:4:4) bilayer at 310 K + (CHARMM36, GROMACS, 667 ns) [NMRlipids simulation 318] alternateName: 200POPC_9000SOL_9SOD_9CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 92 mol%), 9 CLA (4 mol%) and 9 SOD (4 mol%) at 310 K. Simulated with CHARMM36 in GROMACS for 667 ns (53818 atoms). Deposited as NMRlipids Databank simulation 318 and available from https://doi.org/10.5281/zenodo.3434396. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 92 mol%), 9 CLA (4 mol%) and 9 SOD (4 mol%) at 310 K. Simulated with CHARMM36 + in GROMACS for 667 ns (53818 atoms). Deposited as NMRlipids Databank simulation + 318 and available from https://doi.org/10.5281/zenodo.3434396. sameAs: https://doi.org/10.5281/zenodo.3434396 datePublished: '2019-09-17' license: diff --git a/Simulations/722/744/7227444b737b8023a50556d24a364903f2fee400/3623de48284f036bbb63c4806806493d755ce26a/README.yaml b/Simulations/722/744/7227444b737b8023a50556d24a364903f2fee400/3623de48284f036bbb63c4806806493d755ce26a/README.yaml index 455869df3c..9255c59be9 100644 --- a/Simulations/722/744/7227444b737b8023a50556d24a364903f2fee400/3623de48284f036bbb63c4806806493d755ce26a/README.yaml +++ b/Simulations/722/744/7227444b737b8023a50556d24a364903f2fee400/3623de48284f036bbb63c4806806493d755ce26a/README.yaml @@ -49,9 +49,14 @@ SOFTWARE: gromacs DIR_WRK: /usr/home/bort/Databank ID: 358 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (83:9:9) bilayer at 310 K (Slipids for lipids, Kohagen for NaCl, GROMACS 4.6, 100 ns) [NMRlipids simulation 358] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (83:9:9) bilayer at 310 K + (Slipids for lipids, Kohagen for NaCl, GROMACS 4.6, 100 ns) [NMRlipids simulation + 358] alternateName: 200POPC_9000SOL_21SOD_21CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 83 mol%), 21 CLA (9 mol%) and 21 SOD (9 mol%) at 310 K. Simulated with Slipids for lipids, Kohagen for NaCl in GROMACS 4.6 for 100 ns (53842 atoms). Deposited as NMRlipids Databank simulation 358 and available from https://doi.org/10.5281/zenodo.35193. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 83 mol%), 21 CLA (9 mol%) and 21 SOD (9 mol%) at 310 K. Simulated with Slipids + for lipids, Kohagen for NaCl in GROMACS 4.6 for 100 ns (53842 atoms). Deposited + as NMRlipids Databank simulation 358 and available from https://doi.org/10.5281/zenodo.35193. sameAs: https://doi.org/10.5281/zenodo.35193 datePublished: '2015-12-11' license: diff --git a/Simulations/722/744/7227444b737b8023a50556d24a364903f2fee400/671c42892cc90cc0e315085e3fd9e12bb9318ed0/README.yaml b/Simulations/722/744/7227444b737b8023a50556d24a364903f2fee400/671c42892cc90cc0e315085e3fd9e12bb9318ed0/README.yaml index d499e44de8..1c80647c7a 100644 --- a/Simulations/722/744/7227444b737b8023a50556d24a364903f2fee400/671c42892cc90cc0e315085e3fd9e12bb9318ed0/README.yaml +++ b/Simulations/722/744/7227444b737b8023a50556d24a364903f2fee400/671c42892cc90cc0e315085e3fd9e12bb9318ed0/README.yaml @@ -50,9 +50,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 359 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (83:9:9) bilayer at 310 K (Slipids with ECC-scaled ions (Kohagen), GROMACS 4.6, 200 ns) [NMRlipids simulation 359] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (83:9:9) bilayer at 310 K + (Slipids with ECC-scaled ions (Kohagen), GROMACS 4.6, 200 ns) [NMRlipids simulation + 359] alternateName: 200POPC_9000SOL_21SOD_21CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 83 mol%), 21 CLA (9 mol%) and 21 SOD (9 mol%) at 310 K. Simulated with Slipids with ECC-scaled ions (Kohagen) in GROMACS 4.6 for 200 ns (53842 atoms). Deposited as NMRlipids Databank simulation 359 and available from https://doi.org/10.5281/zenodo.259343. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 83 mol%), 21 CLA (9 mol%) and 21 SOD (9 mol%) at 310 K. Simulated with Slipids + with ECC-scaled ions (Kohagen) in GROMACS 4.6 for 200 ns (53842 atoms). Deposited + as NMRlipids Databank simulation 359 and available from https://doi.org/10.5281/zenodo.259343. sameAs: https://doi.org/10.5281/zenodo.259343 datePublished: '2017-01-24' license: @@ -140,7 +145,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.259343 identifier: 10.5281/zenodo.259343 url: https://doi.org/10.5281/zenodo.259343 - name: Popc With Varying Amounts Of Cholesterol, 130 Mm Of Nacl. Slipids With Ecc-Scaled Ions + name: Popc With Varying Amounts Of Cholesterol, 130 Mm Of Nacl. Slipids With Ecc-Scaled + Ions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/725/d82/725d82ea78818f7b0138691a0b1bfcef3c762fc6/82267b5dfeec13dc953dae8ab236fb6b17bbff90/README.yaml b/Simulations/725/d82/725d82ea78818f7b0138691a0b1bfcef3c762fc6/82267b5dfeec13dc953dae8ab236fb6b17bbff90/README.yaml index 9ee04e1603..8b425eeab8 100644 --- a/Simulations/725/d82/725d82ea78818f7b0138691a0b1bfcef3c762fc6/82267b5dfeec13dc953dae8ab236fb6b17bbff90/README.yaml +++ b/Simulations/725/d82/725d82ea78818f7b0138691a0b1bfcef3c762fc6/82267b5dfeec13dc953dae8ab236fb6b17bbff90/README.yaml @@ -50,9 +50,13 @@ SOFTWARE: gromacs DIR_WRK: /usr/home/bort/Databank ID: 517 bioschema_properties: - name: Molecular dynamics trajectory of a CHOL/DAPC (50:50) bilayer at 310 K (CHARMM36, GROMACS, 1000 ns) [NMRlipids simulation 517] + name: Molecular dynamics trajectory of a CHOL/DAPC (50:50) bilayer at 310 K (CHARMM36, + GROMACS, 1000 ns) [NMRlipids simulation 517] alternateName: 144DAPC_144CHOL_11520SOL_310K - description: Molecular dynamics trajectory of a lipid bilayer of 144 CHOL (cholesterol, 50 mol%) and 144 DAPC (1,2-diarachidonoyl-sn-glycero-3-phosphocholine, 50 mol%) at 310 K. Simulated with CHARMM36 in GROMACS for 1000 ns (65088 atoms). Deposited as NMRlipids Databank simulation 517 and available from https://doi.org/10.5281/zenodo.2653721. + description: Molecular dynamics trajectory of a lipid bilayer of 144 CHOL (cholesterol, + 50 mol%) and 144 DAPC (1,2-diarachidonoyl-sn-glycero-3-phosphocholine, 50 mol%) + at 310 K. Simulated with CHARMM36 in GROMACS for 1000 ns (65088 atoms). Deposited + as NMRlipids Databank simulation 517 and available from https://doi.org/10.5281/zenodo.2653721. sameAs: https://doi.org/10.5281/zenodo.2653721 datePublished: '2019-04-29' license: @@ -141,7 +145,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.2653721 identifier: 10.5281/zenodo.2653721 url: https://doi.org/10.5281/zenodo.2653721 - name: Atomistic simulations of cholesterol in symmetric lipid bilayers with varying degrees of lipid chain unsaturation + name: Atomistic simulations of cholesterol in symmetric lipid bilayers with varying + degrees of lipid chain unsaturation publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/72c/a50/72ca507d6c27e37f020ca31197879b41f45a150a/66d5aff21e8512a9bec660eda244715dfd9eebe7/README.yaml b/Simulations/72c/a50/72ca507d6c27e37f020ca31197879b41f45a150a/66d5aff21e8512a9bec660eda244715dfd9eebe7/README.yaml index 3b8fc3d39a..e7627c399f 100644 --- a/Simulations/72c/a50/72ca507d6c27e37f020ca31197879b41f45a150a/66d5aff21e8512a9bec660eda244715dfd9eebe7/README.yaml +++ b/Simulations/72c/a50/72ca507d6c27e37f020ca31197879b41f45a150a/66d5aff21e8512a9bec660eda244715dfd9eebe7/README.yaml @@ -54,9 +54,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 302 bioschema_properties: - name: Molecular dynamics trajectory of a CLA/POPC/POPG/SOD/CAL (32:18:18:18:16) bilayer at 298 K (Slipids, GROMACS, 1000 ns) [NMRlipids simulation 302] + name: Molecular dynamics trajectory of a CLA/POPC/POPG/SOD/CAL (32:18:18:18:16) + bilayer at 298 K (Slipids, GROMACS, 1000 ns) [NMRlipids simulation 302] alternateName: POPCPOPG(1:1)500mM - description: Molecular dynamics trajectory of a lipid bilayer of 230 CLA (32 mol%), 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 18 mol%), 128 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 18 mol%), 128 SOD (18 mol%) and 115 CAL (16 mol%) at 298 K. Simulated with Slipids in GROMACS for 1000 ns (72281 atoms). Deposited as NMRlipids Databank simulation 302 and available from https://doi.org/10.5281/zenodo.3613573. + description: Molecular dynamics trajectory of a lipid bilayer of 230 CLA (32 mol%), + 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 18 mol%), 128 POPG + (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 18 mol%), 128 SOD (18 mol%) + and 115 CAL (16 mol%) at 298 K. Simulated with Slipids in GROMACS for 1000 ns + (72281 atoms). Deposited as NMRlipids Databank simulation 302 and available from + https://doi.org/10.5281/zenodo.3613573. sameAs: https://doi.org/10.5281/zenodo.3613573 datePublished: '2020-01-13' license: @@ -147,7 +153,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3613573 identifier: 10.5281/zenodo.3613573 url: https://doi.org/10.5281/zenodo.3613573 - name: Simulations of POPC:POPG 1:1 membranes with varying levels of CaCl_2 using the Slipids force field + name: Simulations of POPC:POPG 1:1 membranes with varying levels of CaCl_2 using + the Slipids force field publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/72d/1bb/72d1bb7141ef2d9b6f447cefc2c410e82bd8bdb9/14e3a78527c746635c4c6e4861050bf7eab0430a/README.yaml b/Simulations/72d/1bb/72d1bb7141ef2d9b6f447cefc2c410e82bd8bdb9/14e3a78527c746635c4c6e4861050bf7eab0430a/README.yaml index e28c66ad48..02b4a4274d 100644 --- a/Simulations/72d/1bb/72d1bb7141ef2d9b6f447cefc2c410e82bd8bdb9/14e3a78527c746635c4c6e4861050bf7eab0430a/README.yaml +++ b/Simulations/72d/1bb/72d1bb7141ef2d9b6f447cefc2c410e82bd8bdb9/14e3a78527c746635c4c6e4861050bf7eab0430a/README.yaml @@ -57,9 +57,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 526 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CHOL/CAL (40:29:17:14) bilayer at 310 K (Slipids with ECC-scaled ions (Kohagen), GROMACS 4.6, 600 ns) [NMRlipids simulation 526] + name: Molecular dynamics trajectory of a POPC/CLA/CHOL/CAL (40:29:17:14) bilayer + at 310 K (Slipids with ECC-scaled ions (Kohagen), GROMACS 4.6, 600 ns) [NMRlipids + simulation 526] alternateName: 86CHOL_200POPC_9000SOL_73CAL_146CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 40 mol%), 146 CLA (29 mol%), 86 CHOL (cholesterol, 17 mol%) and 73 CAL (14 mol%) at 310 K. Simulated with Slipids with ECC-scaled ions (Kohagen) in GROMACS 4.6 for 600 ns (60383 atoms). Deposited as NMRlipids Databank simulation 526 and available from https://doi.org/10.5281/zenodo.259354. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 40 mol%), 146 CLA (29 mol%), 86 CHOL (cholesterol, 17 mol%) and 73 CAL (14 mol%) + at 310 K. Simulated with Slipids with ECC-scaled ions (Kohagen) in GROMACS 4.6 + for 600 ns (60383 atoms). Deposited as NMRlipids Databank simulation 526 and available + from https://doi.org/10.5281/zenodo.259354. sameAs: https://doi.org/10.5281/zenodo.259354 datePublished: '2017-01-24' license: @@ -149,7 +155,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.259354 identifier: 10.5281/zenodo.259354 url: https://doi.org/10.5281/zenodo.259354 - name: Popc With Varying Amounts Of Cholesterol, 450 Mm Of Cacl_2. Slipids With Ecc-Scaled Ions + name: Popc With Varying Amounts Of Cholesterol, 450 Mm Of Cacl_2. Slipids With + Ecc-Scaled Ions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/738/33d/73833de43d8a0b83bec116c431b935a03fcd2ad1/09cf3e0b2a9abcf53326d9e7f9d041cb917cc60d/README.yaml b/Simulations/738/33d/73833de43d8a0b83bec116c431b935a03fcd2ad1/09cf3e0b2a9abcf53326d9e7f9d041cb917cc60d/README.yaml index 3b36685a13..6039750c52 100644 --- a/Simulations/738/33d/73833de43d8a0b83bec116c431b935a03fcd2ad1/09cf3e0b2a9abcf53326d9e7f9d041cb917cc60d/README.yaml +++ b/Simulations/738/33d/73833de43d8a0b83bec116c431b935a03fcd2ad1/09cf3e0b2a9abcf53326d9e7f9d041cb917cc60d/README.yaml @@ -44,9 +44,13 @@ EXPERIMENT: SLiPC: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a SLiPC bilayer at 333.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 634] + name: Molecular dynamics trajectory of a SLiPC bilayer at 333.15 K (CHARMM36, GROMACS, + 1001 ns) [NMRlipids simulation 634] alternateName: 64SLiPC_3200SOL_333K - description: Molecular dynamics trajectory of a lipid bilayer of 64 SLiPC (1-(18:0)-2-(18:2 $^{\Delta9,12}$)-sn-glycero-3-phosphocholine) at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (18432 atoms). Deposited as NMRlipids Databank simulation 634 and available from https://doi.org/10.5281/zenodo.6943413. + description: Molecular dynamics trajectory of a lipid bilayer of 64 SLiPC (1-(18:0)-2-(18:2 + $^{\Delta9,12}$)-sn-glycero-3-phosphocholine) at 333.15 K. Simulated with CHARMM36 + in GROMACS for 1001 ns (18432 atoms). Deposited as NMRlipids Databank simulation + 634 and available from https://doi.org/10.5281/zenodo.6943413. sameAs: https://doi.org/10.5281/zenodo.6943413 datePublished: '2022-07-30' license: @@ -134,7 +138,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.6943413 identifier: 10.5281/zenodo.6943413 url: https://doi.org/10.5281/zenodo.6943413 - name: Simulations of different single-component bilayers, three different system sizes + name: Simulations of different single-component bilayers, three different system + sizes publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/738/9ea/7389eacdbb94a146555dc6cbcd0164dd94dcf673/ec6eaaf0254f333985a82e3526dec3aba967692a/README.yaml b/Simulations/738/9ea/7389eacdbb94a146555dc6cbcd0164dd94dcf673/ec6eaaf0254f333985a82e3526dec3aba967692a/README.yaml index 2005e6cf78..fab28837f6 100644 --- a/Simulations/738/9ea/7389eacdbb94a146555dc6cbcd0164dd94dcf673/ec6eaaf0254f333985a82e3526dec3aba967692a/README.yaml +++ b/Simulations/738/9ea/7389eacdbb94a146555dc6cbcd0164dd94dcf673/ec6eaaf0254f333985a82e3526dec3aba967692a/README.yaml @@ -55,9 +55,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 427 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (60:27:13) bilayer at 313 K (ECC-lipids, GROMACS 5.1.4, 300 ns) [NMRlipids simulation 427] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (60:27:13) bilayer at 313 + K (ECC-lipids, GROMACS 5.1.4, 300 ns) [NMRlipids simulation 427] alternateName: 128POPC_6400SOL_29CAL_58CLA_313K - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 60 mol%), 58 CLA (27 mol%) and 29 CAL (13 mol%) at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 300 ns (36439 atoms). Deposited as NMRlipids Databank simulation 427 and available from https://doi.org/10.5281/zenodo.3335503. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 60 mol%), 58 CLA (27 mol%) and 29 CAL (13 mol%) at 313 K. Simulated with ECC-lipids + in GROMACS 5.1.4 for 300 ns (36439 atoms). Deposited as NMRlipids Databank simulation + 427 and available from https://doi.org/10.5281/zenodo.3335503. sameAs: https://doi.org/10.5281/zenodo.3335503 datePublished: '2017-12-19' license: @@ -149,7 +153,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3335503 identifier: 10.5281/zenodo.3335503 url: https://doi.org/10.5281/zenodo.3335503 - name: Simulations of POPC lipid bilayer in water solution at various NaCl, KCl and CaCl2 concentrations using ECC-POPC force field + name: Simulations of POPC lipid bilayer in water solution at various NaCl, KCl + and CaCl2 concentrations using ECC-POPC force field publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/73e/223/73e223464a5da222a5b3cf461a06295d52387d41/31d6c113df7563e0164abd1e7c696d9df8740aa4/README.yaml b/Simulations/73e/223/73e223464a5da222a5b3cf461a06295d52387d41/31d6c113df7563e0164abd1e7c696d9df8740aa4/README.yaml index 372f7ae204..d8d403b153 100644 --- a/Simulations/73e/223/73e223464a5da222a5b3cf461a06295d52387d41/31d6c113df7563e0164abd1e7c696d9df8740aa4/README.yaml +++ b/Simulations/73e/223/73e223464a5da222a5b3cf461a06295d52387d41/31d6c113df7563e0164abd1e7c696d9df8740aa4/README.yaml @@ -43,9 +43,13 @@ EXPERIMENT: ID: 607 AUTHORS_CONTACT: Javanainen, Matti bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPE (50:50) bilayer at 298 K (Slipids, GROMACS, 300 ns) [NMRlipids simulation 607] + name: Molecular dynamics trajectory of a POPC/POPE (50:50) bilayer at 298 K (Slipids, + GROMACS, 300 ns) [NMRlipids simulation 607] alternateName: POPCPOPE_(1:1)_T298K - description: Molecular dynamics trajectory of a lipid bilayer of 100 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 50 mol%) and 100 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 50 mol%) at 298 K. Simulated with Slipids in GROMACS for 300 ns (52900 atoms). Deposited as NMRlipids Databank simulation 607 and available from https://doi.org/10.5281/zenodo.3605386. + description: Molecular dynamics trajectory of a lipid bilayer of 100 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 50 mol%) and 100 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, + 50 mol%) at 298 K. Simulated with Slipids in GROMACS for 300 ns (52900 atoms). + Deposited as NMRlipids Databank simulation 607 and available from https://doi.org/10.5281/zenodo.3605386. sameAs: https://doi.org/10.5281/zenodo.3605386 datePublished: '2020-01-12' license: diff --git a/Simulations/740/21f/74021fba83a4969d721686c4a9a7c4d3f58f82c1/48cf8cb1426d6db469e8393739924a622174fd91/README.yaml b/Simulations/740/21f/74021fba83a4969d721686c4a9a7c4d3f58f82c1/48cf8cb1426d6db469e8393739924a622174fd91/README.yaml index 569759d542..becb1f4d51 100644 --- a/Simulations/740/21f/74021fba83a4969d721686c4a9a7c4d3f58f82c1/48cf8cb1426d6db469e8393739924a622174fd91/README.yaml +++ b/Simulations/740/21f/74021fba83a4969d721686c4a9a7c4d3f58f82c1/48cf8cb1426d6db469e8393739924a622174fd91/README.yaml @@ -50,9 +50,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 84 bioschema_properties: - name: Molecular dynamics trajectory of a CLA/POPC/CAL (47:30:23) bilayer at 298.15 K (Lipid14 for lipids and AMBER99SB-ILDN for ions, GROMACS 5.0.3, 100 ns) [NMRlipids simulation 84] + name: Molecular dynamics trajectory of a CLA/POPC/CAL (47:30:23) bilayer at 298.15 + K (Lipid14 for lipids and AMBER99SB-ILDN for ions, GROMACS 5.0.3, 100 ns) [NMRlipids + simulation 84] alternateName: 128POPC_6400SOL_100CAL_200CLA_298K - description: Molecular dynamics trajectory of a lipid bilayer of 200 CLA (47 mol%), 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 30 mol%) and 100 CAL (23 mol%) at 298.15 K. Simulated with Lipid14 for lipids and AMBER99SB-ILDN for ions in GROMACS 5.0.3 for 100 ns (36652 atoms). Deposited as NMRlipids Databank simulation 84 and available from https://doi.org/10.5281/zenodo.35074. + description: Molecular dynamics trajectory of a lipid bilayer of 200 CLA (47 mol%), + 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 30 mol%) and 100 CAL + (23 mol%) at 298.15 K. Simulated with Lipid14 for lipids and AMBER99SB-ILDN for + ions in GROMACS 5.0.3 for 100 ns (36652 atoms). Deposited as NMRlipids Databank + simulation 84 and available from https://doi.org/10.5281/zenodo.35074. sameAs: https://doi.org/10.5281/zenodo.35074 datePublished: '2015-12-09' license: diff --git a/Simulations/743/c36/743c36ad0b4bad2cd26b7abd2ff584f49613424e/dcb93acdf33d8c5ac48ade40e4563f0842c3aa9e/README.yaml b/Simulations/743/c36/743c36ad0b4bad2cd26b7abd2ff584f49613424e/dcb93acdf33d8c5ac48ade40e4563f0842c3aa9e/README.yaml index 79352a5df5..516bff12a7 100644 --- a/Simulations/743/c36/743c36ad0b4bad2cd26b7abd2ff584f49613424e/dcb93acdf33d8c5ac48ade40e4563f0842c3aa9e/README.yaml +++ b/Simulations/743/c36/743c36ad0b4bad2cd26b7abd2ff584f49613424e/dcb93acdf33d8c5ac48ade40e4563f0842c3aa9e/README.yaml @@ -41,9 +41,12 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 541 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 303 K (CHARMM36, GROMACS 5.0.6, 500 ns) [NMRlipids simulation 541] + name: Molecular dynamics trajectory of a POPC bilayer at 303 K (CHARMM36, GROMACS + 5.0.6, 500 ns) [NMRlipids simulation 541] alternateName: 128POPC_4040SOL_10A-switch_v1 - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 303 K. Simulated with CHARMM36 in GROMACS 5.0.6 for 500 ns (29272 atoms). Deposited as NMRlipids Databank simulation 541 and available from https://doi.org/10.5281/zenodo.164203. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 303 K. Simulated with CHARMM36 in GROMACS 5.0.6 for 500 ns (29272 atoms). Deposited + as NMRlipids Databank simulation 541 and available from https://doi.org/10.5281/zenodo.164203. sameAs: https://doi.org/10.5281/zenodo.164203 datePublished: '2016-11-01' license: diff --git a/Simulations/744/21d/74421ddd96de79cfc150c5871bfdd1763b8e2071/1d162355e7a3ddc9094d9c0c1d1da744f3fa4746/README.yaml b/Simulations/744/21d/74421ddd96de79cfc150c5871bfdd1763b8e2071/1d162355e7a3ddc9094d9c0c1d1da744f3fa4746/README.yaml index 5b37691e9e..b6795ca7d4 100644 --- a/Simulations/744/21d/74421ddd96de79cfc150c5871bfdd1763b8e2071/1d162355e7a3ddc9094d9c0c1d1da744f3fa4746/README.yaml +++ b/Simulations/744/21d/74421ddd96de79cfc150c5871bfdd1763b8e2071/1d162355e7a3ddc9094d9c0c1d1da744f3fa4746/README.yaml @@ -57,9 +57,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 339 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL/CHOL (45:33:17:5) bilayer at 310 K (Slipids with default Amber ions parameters (type C0), GROMACS 4.6, 2000 ns) [NMRlipids simulation 339] + name: Molecular dynamics trajectory of a POPC/CLA/CAL/CHOL (45:33:17:5) bilayer + at 310 K (Slipids with default Amber ions parameters (type C0), GROMACS 4.6, 2000 + ns) [NMRlipids simulation 339] alternateName: 22CHOL_200POPC_9000SOL_73CAL_146CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 45 mol%), 146 CLA (33 mol%), 73 CAL (17 mol%) and 22 CHOL (cholesterol, 5 mol%) at 310 K. Simulated with Slipids with default Amber ions parameters (type C0) in GROMACS 4.6 for 2000 ns (55647 atoms). Deposited as NMRlipids Databank simulation 339 and available from https://doi.org/10.5281/zenodo.259349. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 45 mol%), 146 CLA (33 mol%), 73 CAL (17 mol%) and 22 CHOL (cholesterol, 5 mol%) + at 310 K. Simulated with Slipids with default Amber ions parameters (type C0) + in GROMACS 4.6 for 2000 ns (55647 atoms). Deposited as NMRlipids Databank simulation + 339 and available from https://doi.org/10.5281/zenodo.259349. sameAs: https://doi.org/10.5281/zenodo.259349 datePublished: '2017-01-24' license: @@ -149,7 +155,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.259349 identifier: 10.5281/zenodo.259349 url: https://doi.org/10.5281/zenodo.259349 - name: Popc With Varying Amounts Of Cholesterol, 450 Mm Of Cacl_2. Slipids With Default Amber Ions + name: Popc With Varying Amounts Of Cholesterol, 450 Mm Of Cacl_2. Slipids With + Default Amber Ions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/744/965/744965a6e888a992c79b9a61256cf8f086046758/3222964fb29e71891e8b3db41325368094404efc/README.yaml b/Simulations/744/965/744965a6e888a992c79b9a61256cf8f086046758/3222964fb29e71891e8b3db41325368094404efc/README.yaml index c74953587c..c82f37894e 100644 --- a/Simulations/744/965/744965a6e888a992c79b9a61256cf8f086046758/3222964fb29e71891e8b3db41325368094404efc/README.yaml +++ b/Simulations/744/965/744965a6e888a992c79b9a61256cf8f086046758/3222964fb29e71891e8b3db41325368094404efc/README.yaml @@ -54,9 +54,13 @@ EXPERIMENT: BOG: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a DMPC/BOG (60:40) bilayer at 303.15 K (Charmm36, GROMACS 2023.2, 500 ns) [NMRlipids simulation 823] + name: Molecular dynamics trajectory of a DMPC/BOG (60:40) bilayer at 303.15 K (Charmm36, + GROMACS 2023.2, 500 ns) [NMRlipids simulation 823] alternateName: DMPC_BOG_2x3_fh - description: Molecular dynamics trajectory of a lipid bilayer of 102 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine, 60 mol%) and 68 BOG (beta-octyl D-glucopyranoside, 40 mol%) at 303.15 K. Simulated with Charmm36 in GROMACS 2023.2 for 500 ns (47754 atoms). Deposited as NMRlipids Databank simulation 823 and available from https://doi.org/10.5281/zenodo.13881447. + description: Molecular dynamics trajectory of a lipid bilayer of 102 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine, + 60 mol%) and 68 BOG (beta-octyl D-glucopyranoside, 40 mol%) at 303.15 K. Simulated + with Charmm36 in GROMACS 2023.2 for 500 ns (47754 atoms). Deposited as NMRlipids + Databank simulation 823 and available from https://doi.org/10.5281/zenodo.13881447. sameAs: https://doi.org/10.5281/zenodo.13881447 datePublished: '2024-10-02' license: diff --git a/Simulations/744/ed2/744ed265f5ec9eefb48da656a79c1883c8f85c6c/9b31adf0381afa9adfcb6a8ca5855fe73d8a8979/README.yaml b/Simulations/744/ed2/744ed265f5ec9eefb48da656a79c1883c8f85c6c/9b31adf0381afa9adfcb6a8ca5855fe73d8a8979/README.yaml index 69e45b824a..6447e0270c 100644 --- a/Simulations/744/ed2/744ed265f5ec9eefb48da656a79c1883c8f85c6c/9b31adf0381afa9adfcb6a8ca5855fe73d8a8979/README.yaml +++ b/Simulations/744/ed2/744ed265f5ec9eefb48da656a79c1883c8f85c6c/9b31adf0381afa9adfcb6a8ca5855fe73d8a8979/README.yaml @@ -45,9 +45,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 800 bioschema_properties: - name: Molecular dynamics trajectory of a DMPC bilayer at 314 K (CHARMM36, GROMACS 2022.2, 350 ns) [NMRlipids simulation 800] + name: Molecular dynamics trajectory of a DMPC bilayer at 314 K (CHARMM36, GROMACS + 2022.2, 350 ns) [NMRlipids simulation 800] alternateName: 200DMPC_1kSOL_300K - description: Molecular dynamics trajectory of a lipid bilayer of 200 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) at 314 K. Simulated with CHARMM36 in GROMACS 2022.2 for 350 ns (26600 atoms). Deposited as NMRlipids Databank simulation 800 and available from https://doi.org/10.5281/zenodo.10958132. + description: Molecular dynamics trajectory of a lipid bilayer of 200 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) + at 314 K. Simulated with CHARMM36 in GROMACS 2022.2 for 350 ns (26600 atoms). + Deposited as NMRlipids Databank simulation 800 and available from https://doi.org/10.5281/zenodo.10958132. sameAs: https://doi.org/10.5281/zenodo.10958132 datePublished: '2024-04-11' license: diff --git a/Simulations/745/bad/745bad0b0de2ec73e911515d768eeaa840003d1c/2550786d5679f11478db96c5a06a506c22ca4b1a/README.yaml b/Simulations/745/bad/745bad0b0de2ec73e911515d768eeaa840003d1c/2550786d5679f11478db96c5a06a506c22ca4b1a/README.yaml index 354a574da4..579b805cc7 100644 --- a/Simulations/745/bad/745bad0b0de2ec73e911515d768eeaa840003d1c/2550786d5679f11478db96c5a06a506c22ca4b1a/README.yaml +++ b/Simulations/745/bad/745bad0b0de2ec73e911515d768eeaa840003d1c/2550786d5679f11478db96c5a06a506c22ca4b1a/README.yaml @@ -41,9 +41,12 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 205 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC bilayer at 338 K (CHARMM36, GROMACS 2016.4, 49 ns) [NMRlipids simulation 205] + name: Molecular dynamics trajectory of a DPPC bilayer at 338 K (CHARMM36, GROMACS + 2016.4, 49 ns) [NMRlipids simulation 205] alternateName: 212DPPC_29826SOL_338K - description: Molecular dynamics trajectory of a lipid bilayer of 212 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) at 338 K. Simulated with CHARMM36 in GROMACS 2016.4 for 49 ns (117038 atoms). Deposited as NMRlipids Databank simulation 205 and available from https://doi.org/10.5281/zenodo.3950029. + description: Molecular dynamics trajectory of a lipid bilayer of 212 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) + at 338 K. Simulated with CHARMM36 in GROMACS 2016.4 for 49 ns (117038 atoms). + Deposited as NMRlipids Databank simulation 205 and available from https://doi.org/10.5281/zenodo.3950029. sameAs: https://doi.org/10.5281/zenodo.3950029 datePublished: '2020-07-20' license: @@ -143,7 +146,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3950029 identifier: 10.5281/zenodo.3950029 url: https://doi.org/10.5281/zenodo.3950029 - name: 212 DPPC Molecules bilayer in pure Water, simulated at temperatures ranging from 288K to 358K + name: 212 DPPC Molecules bilayer in pure Water, simulated at temperatures ranging + from 288K to 358K publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/748/a5b/748a5ba5b6852e2cfdb28b0665ce146cf5ed8a2e/748a5ba5b6852e2cfdb28b0665ce146cf5ed8a2e/README.yaml b/Simulations/748/a5b/748a5ba5b6852e2cfdb28b0665ce146cf5ed8a2e/748a5ba5b6852e2cfdb28b0665ce146cf5ed8a2e/README.yaml index fb5931855f..fb3fbc2031 100644 --- a/Simulations/748/a5b/748a5ba5b6852e2cfdb28b0665ce146cf5ed8a2e/748a5ba5b6852e2cfdb28b0665ce146cf5ed8a2e/README.yaml +++ b/Simulations/748/a5b/748a5ba5b6852e2cfdb28b0665ce146cf5ed8a2e/748a5ba5b6852e2cfdb28b0665ce146cf5ed8a2e/README.yaml @@ -44,9 +44,13 @@ EXPERIMENT: PAPC: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a PAPC/CLA/POT (92:4:4) bilayer at 303.15 K (CHARMM36m, NAMD 3.0, 500 ns) [NMRlipids simulation 907] + name: Molecular dynamics trajectory of a PAPC/CLA/POT (92:4:4) bilayer at 303.15 + K (CHARMM36m, NAMD 3.0, 500 ns) [NMRlipids simulation 907] alternateName: PAPC 16:0 Deu - description: Molecular dynamics trajectory of a lipid bilayer of 200 PAPC (1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine, 92 mol%), 9 CLA (4 mol%) and 9 POT (4 mol%) at 303.15 K. Simulated with CHARMM36m in NAMD 3.0 for 500 ns (53818 atoms). Deposited as NMRlipids Databank simulation 907 and available from https://doi.org/10.5281/zenodo.18471806. + description: Molecular dynamics trajectory of a lipid bilayer of 200 PAPC (1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine, + 92 mol%), 9 CLA (4 mol%) and 9 POT (4 mol%) at 303.15 K. Simulated with CHARMM36m + in NAMD 3.0 for 500 ns (53818 atoms). Deposited as NMRlipids Databank simulation + 907 and available from https://doi.org/10.5281/zenodo.18471806. sameAs: https://doi.org/10.5281/zenodo.18471806 datePublished: '2026-02-03' license: @@ -137,7 +141,9 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.18471806 identifier: 10.5281/zenodo.18471806 url: https://doi.org/10.5281/zenodo.18471806 - name: 'PAPC lipid bilayer: 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine (16:0)(20:4) | Deutrated, 16:0 | 303K, CHARMM36m-WYF forcefield, NAMD 3.0.2, 2* 500 ns' + name: 'PAPC lipid bilayer: 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine + (16:0)(20:4) | Deutrated, 16:0 | 303K, CHARMM36m-WYF forcefield, NAMD 3.0.2, + 2* 500 ns' publisher: Zenodo _source: api: datacite diff --git a/Simulations/74f/eeb/74feeb08b7b5b2dcf54639ef1c51b9d2c4731c81/17067c369e136d719304061da5b010059645e3bf/README.yaml b/Simulations/74f/eeb/74feeb08b7b5b2dcf54639ef1c51b9d2c4731c81/17067c369e136d719304061da5b010059645e3bf/README.yaml index 41b0e03f6f..ff79a8a726 100644 --- a/Simulations/74f/eeb/74feeb08b7b5b2dcf54639ef1c51b9d2c4731c81/17067c369e136d719304061da5b010059645e3bf/README.yaml +++ b/Simulations/74f/eeb/74feeb08b7b5b2dcf54639ef1c51b9d2c4731c81/17067c369e136d719304061da5b010059645e3bf/README.yaml @@ -41,9 +41,12 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 98 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 303 K (CHARMM36, GROMACS 5.0.6, 500 ns) [NMRlipids simulation 98] + name: Molecular dynamics trajectory of a POPC bilayer at 303 K (CHARMM36, GROMACS + 5.0.6, 500 ns) [NMRlipids simulation 98] alternateName: 128POPC_5120SOL_8A-switch_v2 - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 303 K. Simulated with CHARMM36 in GROMACS 5.0.6 for 500 ns (32512 atoms). Deposited as NMRlipids Databank simulation 98 and available from https://doi.org/10.5281/zenodo.164206. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 303 K. Simulated with CHARMM36 in GROMACS 5.0.6 for 500 ns (32512 atoms). Deposited + as NMRlipids Databank simulation 98 and available from https://doi.org/10.5281/zenodo.164206. sameAs: https://doi.org/10.5281/zenodo.164206 datePublished: '2016-11-01' license: diff --git a/Simulations/752/7ec/7527ecdcca76b1db5593639e4e84069b65570f68/5fe5e17ca65737161140a6149290095af1f7056f/README.yaml b/Simulations/752/7ec/7527ecdcca76b1db5593639e4e84069b65570f68/5fe5e17ca65737161140a6149290095af1f7056f/README.yaml index b97b698fa8..2967226e14 100644 --- a/Simulations/752/7ec/7527ecdcca76b1db5593639e4e84069b65570f68/5fe5e17ca65737161140a6149290095af1f7056f/README.yaml +++ b/Simulations/752/7ec/7527ecdcca76b1db5593639e4e84069b65570f68/5fe5e17ca65737161140a6149290095af1f7056f/README.yaml @@ -42,9 +42,12 @@ EXPERIMENT: - 10.1016/j.bbamem.2011.07.022/2 ID: 602 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 303 K (GAFFlipid, GROMACS 4.5, 32 ns) [NMRlipids simulation 602] + name: Molecular dynamics trajectory of a POPC bilayer at 303 K (GAFFlipid, GROMACS + 4.5, 32 ns) [NMRlipids simulation 602] alternateName: 126POPC_3948SOL_303K - description: Molecular dynamics trajectory of a lipid bilayer of 126 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 303 K. Simulated with GAFFlipid in GROMACS 4.5 for 32 ns (28728 atoms). Deposited as NMRlipids Databank simulation 602 and available from https://doi.org/10.5281/zenodo.5734452. + description: Molecular dynamics trajectory of a lipid bilayer of 126 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 303 K. Simulated with GAFFlipid in GROMACS 4.5 for 32 ns (28728 atoms). Deposited + as NMRlipids Databank simulation 602 and available from https://doi.org/10.5281/zenodo.5734452. sameAs: https://doi.org/10.5281/zenodo.5734452 datePublished: '2015-01-07' license: @@ -133,7 +136,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.5734452 identifier: 10.5281/zenodo.5734452 url: https://doi.org/10.5281/zenodo.5734452 - name: MD simulation trajectory and related files for POPC bilayer (GAFFlipid, Gromacs 4.5) + name: MD simulation trajectory and related files for POPC bilayer (GAFFlipid, + Gromacs 4.5) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/752/c18/752c1875f486af80ad43f8e73d251d20b4f00c2d/a4e58098c3f152f08655244499f8ef4f5a57d131/README.yaml b/Simulations/752/c18/752c1875f486af80ad43f8e73d251d20b4f00c2d/a4e58098c3f152f08655244499f8ef4f5a57d131/README.yaml index 75791a5346..6e524d56a0 100644 --- a/Simulations/752/c18/752c1875f486af80ad43f8e73d251d20b4f00c2d/a4e58098c3f152f08655244499f8ef4f5a57d131/README.yaml +++ b/Simulations/752/c18/752c1875f486af80ad43f8e73d251d20b4f00c2d/a4e58098c3f152f08655244499f8ef4f5a57d131/README.yaml @@ -63,9 +63,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 603 bioschema_properties: - name: Molecular dynamics trajectory of a CLA/POPC/CAL/POPS (36:33:23:8) bilayer at 310 K (Berger, GROMACS 4.5.5, 100 ns) [NMRlipids simulation 603] + name: Molecular dynamics trajectory of a CLA/POPC/CAL/POPS (36:33:23:8) bilayer + at 310 K (Berger, GROMACS 4.5.5, 100 ns) [NMRlipids simulation 603] alternateName: 104POPC_24POPS_4306SOL_72CAL_112CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 112 CLA (36 mol%), 104 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 33 mol%), 72 CAL (23 mol%) and 24 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 8 mol%) at 310 K. Simulated with Berger in GROMACS 4.5.5 for 100 ns (19830 atoms). Deposited as NMRlipids Databank simulation 603 and available from https://doi.org/10.5281/zenodo.887400. + description: Molecular dynamics trajectory of a lipid bilayer of 112 CLA (36 mol%), + 104 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 33 mol%), 72 CAL (23 + mol%) and 24 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 8 mol%) + at 310 K. Simulated with Berger in GROMACS 4.5.5 for 100 ns (19830 atoms). Deposited + as NMRlipids Databank simulation 603 and available from https://doi.org/10.5281/zenodo.887400. sameAs: https://doi.org/10.5281/zenodo.887400 datePublished: '2017-09-07' license: @@ -158,7 +163,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.887400 identifier: 10.5281/zenodo.887400 url: https://doi.org/10.5281/zenodo.887400 - name: Md Simulation Trajectory Of A Popc/Pops (4:1) Bilayer With 715Mm Cacl2, Berger Force Field For Lipids, Scaled Charges For Ca2+ And Cl- + name: Md Simulation Trajectory Of A Popc/Pops (4:1) Bilayer With 715Mm Cacl2, + Berger Force Field For Lipids, Scaled Charges For Ca2+ And Cl- publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/755/0bd/7550bdc00ca714d8b1ebc30840d4aebedbe9be39/ae4fd11bba4254956cf2888eed26d8778af27e13/README.yaml b/Simulations/755/0bd/7550bdc00ca714d8b1ebc30840d4aebedbe9be39/ae4fd11bba4254956cf2888eed26d8778af27e13/README.yaml index 78b2fa8853..78a2e325cf 100644 --- a/Simulations/755/0bd/7550bdc00ca714d8b1ebc30840d4aebedbe9be39/ae4fd11bba4254956cf2888eed26d8778af27e13/README.yaml +++ b/Simulations/755/0bd/7550bdc00ca714d8b1ebc30840d4aebedbe9be39/ae4fd11bba4254956cf2888eed26d8778af27e13/README.yaml @@ -56,9 +56,14 @@ EXPERIMENT: SM16: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a POPC/SM16/ERG (35:35:30) bilayer at 295 K (Slipids, GROMACS 2019.6, 100 ns) [NMRlipids simulation 847] + name: Molecular dynamics trajectory of a POPC/SM16/ERG (35:35:30) bilayer at 295 + K (Slipids, GROMACS 2019.6, 100 ns) [NMRlipids simulation 847] alternateName: POPC/SM16/ERG(35:35:30) - description: Molecular dynamics trajectory of a lipid bilayer of 360 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 35 mol%), 352 SM16 (N-palmitoyl-D-erythro-sphingosylphosphorylcholine, 35 mol%) and 304 ERG (ergosterol, 30 mol%) at 295 K. Simulated with Slipids in GROMACS 2019.6 for 100 ns (222656 atoms). Deposited as NMRlipids Databank simulation 847 and available from https://doi.org/10.5281/zenodo.17730735. + description: Molecular dynamics trajectory of a lipid bilayer of 360 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 35 mol%), 352 SM16 (N-palmitoyl-D-erythro-sphingosylphosphorylcholine, 35 mol%) + and 304 ERG (ergosterol, 30 mol%) at 295 K. Simulated with Slipids in GROMACS + 2019.6 for 100 ns (222656 atoms). Deposited as NMRlipids Databank simulation 847 + and available from https://doi.org/10.5281/zenodo.17730735. sameAs: https://doi.org/10.5281/zenodo.17730735 datePublished: '2025-11-27' license: @@ -154,7 +159,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.17730735 identifier: 10.5281/zenodo.17730735 url: https://doi.org/10.5281/zenodo.17730735 - name: 'MD simulation trajectory of Ternary mixture of POPC/PSM/Ergo (35:35:30) at 295 K: Slipids, GROMACS 2019.6' + name: 'MD simulation trajectory of Ternary mixture of POPC/PSM/Ergo (35:35:30) + at 295 K: Slipids, GROMACS 2019.6' publisher: Zenodo _source: api: datacite diff --git a/Simulations/75b/d62/75bd625d0c29f45c4b3a1bc107df9122abc270be/a6ac2c52a4fe03bc145c34c7d9c759840702e6b1/README.yaml b/Simulations/75b/d62/75bd625d0c29f45c4b3a1bc107df9122abc270be/a6ac2c52a4fe03bc145c34c7d9c759840702e6b1/README.yaml index 5779ce8459..2bb89e5513 100644 --- a/Simulations/75b/d62/75bd625d0c29f45c4b3a1bc107df9122abc270be/a6ac2c52a4fe03bc145c34c7d9c759840702e6b1/README.yaml +++ b/Simulations/75b/d62/75bd625d0c29f45c4b3a1bc107df9122abc270be/a6ac2c52a4fe03bc145c34c7d9c759840702e6b1/README.yaml @@ -50,9 +50,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/3 ID: 695 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (89:11) bilayer at 298.15 K (MacRog, GROMACS 2021, 1001 ns) [NMRlipids simulation 695] + name: Molecular dynamics trajectory of a POPC/CHOL (89:11) bilayer at 298.15 K (MacRog, + GROMACS 2021, 1001 ns) [NMRlipids simulation 695] alternateName: MacRog_POPC_CHOL11_M - description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 89 mol%) and 32 CHOL (cholesterol, 11 mol%) at 298.15 K. Simulated with MacRog in GROMACS 2021 for 1001 ns (79872 atoms). Deposited as NMRlipids Databank simulation 695 and available from https://doi.org/10.5281/zenodo.7061800. + description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 89 mol%) and 32 CHOL (cholesterol, 11 mol%) at 298.15 K. Simulated with MacRog + in GROMACS 2021 for 1001 ns (79872 atoms). Deposited as NMRlipids Databank simulation + 695 and available from https://doi.org/10.5281/zenodo.7061800. sameAs: https://doi.org/10.5281/zenodo.7061800 datePublished: '2022-09-08' license: diff --git a/Simulations/764/ddd/764dddf7870cc2563bdb74f5b2812b1004ecb63b/bdd86df237be0af314ed4de8ddeb90252d3636af/README.yaml b/Simulations/764/ddd/764dddf7870cc2563bdb74f5b2812b1004ecb63b/bdd86df237be0af314ed4de8ddeb90252d3636af/README.yaml index 460a4a1725..a44196f683 100644 --- a/Simulations/764/ddd/764dddf7870cc2563bdb74f5b2812b1004ecb63b/bdd86df237be0af314ed4de8ddeb90252d3636af/README.yaml +++ b/Simulations/764/ddd/764dddf7870cc2563bdb74f5b2812b1004ecb63b/bdd86df237be0af314ed4de8ddeb90252d3636af/README.yaml @@ -41,9 +41,12 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 554 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 303 K (CHARMM36, GROMACS 5.0.6, 500 ns) [NMRlipids simulation 554] + name: Molecular dynamics trajectory of a POPC bilayer at 303 K (CHARMM36, GROMACS + 5.0.6, 500 ns) [NMRlipids simulation 554] alternateName: 128POPC_5120SOL_8A-switch_v1 - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 303 K. Simulated with CHARMM36 in GROMACS 5.0.6 for 500 ns (32512 atoms). Deposited as NMRlipids Databank simulation 554 and available from https://doi.org/10.5281/zenodo.164206. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 303 K. Simulated with CHARMM36 in GROMACS 5.0.6 for 500 ns (32512 atoms). Deposited + as NMRlipids Databank simulation 554 and available from https://doi.org/10.5281/zenodo.164206. sameAs: https://doi.org/10.5281/zenodo.164206 datePublished: '2016-11-01' license: diff --git a/Simulations/767/5cb/7675cbdb48b9aa08e7b6111a485ac1698ccbd808/35501524f7aef295dd214c3140014935bf50ad76/README.yaml b/Simulations/767/5cb/7675cbdb48b9aa08e7b6111a485ac1698ccbd808/35501524f7aef295dd214c3140014935bf50ad76/README.yaml index 7ac7100002..33a3386aa4 100644 --- a/Simulations/767/5cb/7675cbdb48b9aa08e7b6111a485ac1698ccbd808/35501524f7aef295dd214c3140014935bf50ad76/README.yaml +++ b/Simulations/767/5cb/7675cbdb48b9aa08e7b6111a485ac1698ccbd808/35501524f7aef295dd214c3140014935bf50ad76/README.yaml @@ -57,9 +57,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 435 bioschema_properties: - name: Molecular dynamics trajectory of a POPE/SOD/POPG/CLA (52:24:17:7) bilayer at 310 K (Slipids, GROMACS 5.1.2, 100 ns) [NMRlipids simulation 435] + name: Molecular dynamics trajectory of a POPE/SOD/POPG/CLA (52:24:17:7) bilayer + at 310 K (Slipids, GROMACS 5.1.2, 100 ns) [NMRlipids simulation 435] alternateName: 126POPG_374POPE_25000SOL_176SOD_50CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 374 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 52 mol%), 176 SOD (24 mol%), 126 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 17 mol%) and 50 CLA (7 mol%) at 310 K. Simulated with Slipids in GROMACS 5.1.2 for 100 ns (137978 atoms). Deposited as NMRlipids Databank simulation 435 and available from https://doi.org/10.5281/zenodo.2579224. + description: Molecular dynamics trajectory of a lipid bilayer of 374 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, + 52 mol%), 176 SOD (24 mol%), 126 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, + 17 mol%) and 50 CLA (7 mol%) at 310 K. Simulated with Slipids in GROMACS 5.1.2 + for 100 ns (137978 atoms). Deposited as NMRlipids Databank simulation 435 and + available from https://doi.org/10.5281/zenodo.2579224. sameAs: https://doi.org/10.5281/zenodo.2579224 datePublished: '2019-02-27' license: @@ -152,7 +157,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.2579224 identifier: 10.5281/zenodo.2579224 url: https://doi.org/10.5281/zenodo.2579224 - name: SLIPID POPG-POPE 1:3 Bilayer Simulation (Last 100 ns, 150 mM NaCl, 310 K ) + name: SLIPID POPG-POPE 1:3 Bilayer Simulation (Last 100 ns, 150 mM NaCl, 310 K + ) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/774/f33/774f336bba838c0e53707605eaf2f8d8e4de6886/58c0154cde7ecaa3ce09e3a28f23bda4c4029d7e/README.yaml b/Simulations/774/f33/774f336bba838c0e53707605eaf2f8d8e4de6886/58c0154cde7ecaa3ce09e3a28f23bda4c4029d7e/README.yaml index 2afa4fc19e..846c253092 100644 --- a/Simulations/774/f33/774f336bba838c0e53707605eaf2f8d8e4de6886/58c0154cde7ecaa3ce09e3a28f23bda4c4029d7e/README.yaml +++ b/Simulations/774/f33/774f336bba838c0e53707605eaf2f8d8e4de6886/58c0154cde7ecaa3ce09e3a28f23bda4c4029d7e/README.yaml @@ -41,9 +41,12 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 375 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 303 K (CHARMM36, GROMACS 4.5, 20 ns) [NMRlipids simulation 375] + name: Molecular dynamics trajectory of a POPC bilayer at 303 K (CHARMM36, GROMACS + 4.5, 20 ns) [NMRlipids simulation 375] alternateName: 72POPC_504SOL_303K - description: Molecular dynamics trajectory of a lipid bilayer of 72 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 303 K. Simulated with CHARMM36 in GROMACS 4.5 for 20 ns (11160 atoms). Deposited as NMRlipids Databank simulation 375 and available from https://doi.org/10.5281/zenodo.13945. + description: Molecular dynamics trajectory of a lipid bilayer of 72 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 303 K. Simulated with CHARMM36 in GROMACS 4.5 for 20 ns (11160 atoms). Deposited + as NMRlipids Databank simulation 375 and available from https://doi.org/10.5281/zenodo.13945. sameAs: https://doi.org/10.5281/zenodo.13945 datePublished: '2015-01-14' license: @@ -128,7 +131,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.13945 identifier: 10.5281/zenodo.13945 url: https://doi.org/10.5281/zenodo.13945 - name: Md Simulation Trajectory And Related Files For Popc Bilayer In Low Hydration (Charmm36, Gromacs 4.5) + name: Md Simulation Trajectory And Related Files For Popc Bilayer In Low Hydration + (Charmm36, Gromacs 4.5) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/77e/38d/77e38d061e430bacd93ad084965c5befa5a58d8f/77e38d061e430bacd93ad084965c5befa5a58d8f/README.yaml b/Simulations/77e/38d/77e38d061e430bacd93ad084965c5befa5a58d8f/77e38d061e430bacd93ad084965c5befa5a58d8f/README.yaml index df1552a178..997df4f1c2 100644 --- a/Simulations/77e/38d/77e38d061e430bacd93ad084965c5befa5a58d8f/77e38d061e430bacd93ad084965c5befa5a58d8f/README.yaml +++ b/Simulations/77e/38d/77e38d061e430bacd93ad084965c5befa5a58d8f/77e38d061e430bacd93ad084965c5befa5a58d8f/README.yaml @@ -46,9 +46,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 744 bioschema_properties: - name: Molecular dynamics trajectory of a CLA/POPC/CAL (43:36:21) bilayer at 303 K (Charmm-Drude polarizable; system has been equilibriated using Charmm36, OPENMM 7.4.1, 517 ns) [NMRlipids simulation 744] + name: Molecular dynamics trajectory of a CLA/POPC/CAL (43:36:21) bilayer at 303 + K (Charmm-Drude polarizable; system has been equilibriated using Charmm36, OPENMM + 7.4.1, 517 ns) [NMRlipids simulation 744] alternateName: 128POPC_6400SOL_76CaCl2_303K - description: Molecular dynamics trajectory of a lipid bilayer of 152 CLA (43 mol%), 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 36 mol%) and 76 CAL (21 mol%) at 303 K. Simulated with Charmm-Drude polarizable; system has been equilibriated using Charmm36 in OPENMM 7.4.1 for 517 ns (57288 atoms). Deposited as NMRlipids Databank simulation 744 and available from https://doi.org/10.5281/zenodo.7604040. + description: Molecular dynamics trajectory of a lipid bilayer of 152 CLA (43 mol%), + 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 36 mol%) and 76 CAL + (21 mol%) at 303 K. Simulated with Charmm-Drude polarizable; system has been equilibriated + using Charmm36 in OPENMM 7.4.1 for 517 ns (57288 atoms). Deposited as NMRlipids + Databank simulation 744 and available from https://doi.org/10.5281/zenodo.7604040. sameAs: https://doi.org/10.5281/zenodo.7604040 datePublished: '2020-08-21' license: @@ -140,7 +146,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.7604040 identifier: 10.5281/zenodo.7604040 url: https://doi.org/10.5281/zenodo.7604040 - name: Pure POPC Membrane with 650mM CaCl2 simulations using Drude Polarizable Force Field and OpenMM + name: Pure POPC Membrane with 650mM CaCl2 simulations using Drude Polarizable + Force Field and OpenMM publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/780/d37/780d3763c456a6837a6d65f48cc7e7b14e4a3a6e/780d3763c456a6837a6d65f48cc7e7b14e4a3a6e/README.yaml b/Simulations/780/d37/780d3763c456a6837a6d65f48cc7e7b14e4a3a6e/780d3763c456a6837a6d65f48cc7e7b14e4a3a6e/README.yaml index c65edb520d..5af676f45d 100644 --- a/Simulations/780/d37/780d3763c456a6837a6d65f48cc7e7b14e4a3a6e/780d3763c456a6837a6d65f48cc7e7b14e4a3a6e/README.yaml +++ b/Simulations/780/d37/780d3763c456a6837a6d65f48cc7e7b14e4a3a6e/780d3763c456a6837a6d65f48cc7e7b14e4a3a6e/README.yaml @@ -40,9 +40,12 @@ EXPERIMENT: FORMFACTOR: - 10.1016/j.bbamem.2011.07.022/2 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 303 K (Charmm-Drude polarizable2023, OPENMM, 200 ns) [NMRlipids simulation 752] + name: Molecular dynamics trajectory of a POPC bilayer at 303 K (Charmm-Drude polarizable2023, + OPENMM, 200 ns) [NMRlipids simulation 752] alternateName: POPC_CHARMMdrude2023_303K - description: Molecular dynamics trajectory of a lipid bilayer of 72 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 303 K. Simulated with Charmm-Drude polarizable2023 in OPENMM for 200 ns (25163 atoms). Deposited as NMRlipids Databank simulation 752 and available from https://doi.org/10.5281/zenodo.7916287. + description: Molecular dynamics trajectory of a lipid bilayer of 72 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 303 K. Simulated with Charmm-Drude polarizable2023 in OPENMM for 200 ns (25163 + atoms). Deposited as NMRlipids Databank simulation 752 and available from https://doi.org/10.5281/zenodo.7916287. sameAs: https://doi.org/10.5281/zenodo.7916287 datePublished: '2023-05-09' license: @@ -130,7 +133,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.7916287 identifier: 10.5281/zenodo.7916287 url: https://doi.org/10.5281/zenodo.7916287 - name: OpenMM simulations of POPC using the CHARMM Drude2023 force field in xtc format + name: OpenMM simulations of POPC using the CHARMM Drude2023 force field in xtc + format publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/785/ea1/785ea16d65161e6ae5d5bf3018f6c3f2540b4826/8227880b80c102d686b502adeecbbf73e0768b74/README.yaml b/Simulations/785/ea1/785ea16d65161e6ae5d5bf3018f6c3f2540b4826/8227880b80c102d686b502adeecbbf73e0768b74/README.yaml index 742f9c59c3..fc852783c3 100644 --- a/Simulations/785/ea1/785ea16d65161e6ae5d5bf3018f6c3f2540b4826/8227880b80c102d686b502adeecbbf73e0768b74/README.yaml +++ b/Simulations/785/ea1/785ea16d65161e6ae5d5bf3018f6c3f2540b4826/8227880b80c102d686b502adeecbbf73e0768b74/README.yaml @@ -71,9 +71,16 @@ EXPERIMENT: POPE: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a POT/SAPC/POPE/DLIPA/DLIPG/CLA (30:23:18:10:10:9) bilayer at 310 K (CHARMM36, GROMACS 2024, 1000 ns) [NMRlipids simulation 840] + name: Molecular dynamics trajectory of a POT/SAPC/POPE/DLIPA/DLIPG/CLA (30:23:18:10:10:9) + bilayer at 310 K (CHARMM36, GROMACS 2024, 1000 ns) [NMRlipids simulation 840] alternateName: IMM_TLCL_divided_PA_PG_310K - description: Molecular dynamics trajectory of a lipid bilayer of 117 POT (30 mol%), 90 SAPC (1-stearoyl-2-arachidonoyl-sn-glycero-3-phosphocholine, 23 mol%), 70 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 18 mol%), 40 DLIPA (1,2-dilinoleoyl-sn-glycero-3-phosphate, 10 mol%), 40 DLIPG (1,2-dilinoleoyl-sn-glycero-3-phosphoglycerol, 10 mol%) and 37 CLA (9 mol%) at 310 K. Simulated with CHARMM36 in GROMACS 2024 for 1000 ns (73866 atoms). Deposited as NMRlipids Databank simulation 840 and available from https://doi.org/10.5281/zenodo.16813252. + description: Molecular dynamics trajectory of a lipid bilayer of 117 POT (30 mol%), + 90 SAPC (1-stearoyl-2-arachidonoyl-sn-glycero-3-phosphocholine, 23 mol%), 70 POPE + (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 18 mol%), 40 DLIPA (1,2-dilinoleoyl-sn-glycero-3-phosphate, + 10 mol%), 40 DLIPG (1,2-dilinoleoyl-sn-glycero-3-phosphoglycerol, 10 mol%) and + 37 CLA (9 mol%) at 310 K. Simulated with CHARMM36 in GROMACS 2024 for 1000 ns + (73866 atoms). Deposited as NMRlipids Databank simulation 840 and available from + https://doi.org/10.5281/zenodo.16813252. sameAs: https://doi.org/10.5281/zenodo.16813252 datePublished: '2025-08-12' license: @@ -178,7 +185,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.16813252 identifier: 10.5281/zenodo.16813252 url: https://doi.org/10.5281/zenodo.16813252 - name: Simulation of model mitochondrial membrane where TLCL is divided into TLPA+PG (CHARMM36) + name: Simulation of model mitochondrial membrane where TLCL is divided into TLPA+PG + (CHARMM36) publisher: Zenodo _source: api: datacite diff --git a/Simulations/789/93b/78993b7c956b4537f5e112686c66599ffaef5a9e/3cb775e3767ddb5b8616bd831c850b1e6959fafa/README.yaml b/Simulations/789/93b/78993b7c956b4537f5e112686c66599ffaef5a9e/3cb775e3767ddb5b8616bd831c850b1e6959fafa/README.yaml index 419c326b83..9a335030e6 100644 --- a/Simulations/789/93b/78993b7c956b4537f5e112686c66599ffaef5a9e/3cb775e3767ddb5b8616bd831c850b1e6959fafa/README.yaml +++ b/Simulations/789/93b/78993b7c956b4537f5e112686c66599ffaef5a9e/3cb775e3767ddb5b8616bd831c850b1e6959fafa/README.yaml @@ -49,9 +49,14 @@ SOFTWARE: gromacs DIR_WRK: /usr/home/bort/Databank ID: 559 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (38:31:31) bilayer at 310 K (Slipids for lipids, Kohagen for NaCl, GROMACS 4.6, 100 ns) [NMRlipids simulation 559] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (38:31:31) bilayer at 310 + K (Slipids for lipids, Kohagen for NaCl, GROMACS 4.6, 100 ns) [NMRlipids simulation + 559] alternateName: 200POPC_9000SOL_162SOD_162CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 38 mol%), 162 CLA (31 mol%) and 162 SOD (31 mol%) at 310 K. Simulated with Slipids for lipids, Kohagen for NaCl in GROMACS 4.6 for 100 ns (54124 atoms). Deposited as NMRlipids Databank simulation 559 and available from https://doi.org/10.5281/zenodo.35193. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 38 mol%), 162 CLA (31 mol%) and 162 SOD (31 mol%) at 310 K. Simulated with Slipids + for lipids, Kohagen for NaCl in GROMACS 4.6 for 100 ns (54124 atoms). Deposited + as NMRlipids Databank simulation 559 and available from https://doi.org/10.5281/zenodo.35193. sameAs: https://doi.org/10.5281/zenodo.35193 datePublished: '2015-12-11' license: diff --git a/Simulations/796/744/79674488b4dc2a187d15a72990d640df2a8eef83/41a84d1d8029340f67148f65751a8fbefb08c455/README.yaml b/Simulations/796/744/79674488b4dc2a187d15a72990d640df2a8eef83/41a84d1d8029340f67148f65751a8fbefb08c455/README.yaml index 11313ba04f..eb40afca86 100644 --- a/Simulations/796/744/79674488b4dc2a187d15a72990d640df2a8eef83/41a84d1d8029340f67148f65751a8fbefb08c455/README.yaml +++ b/Simulations/796/744/79674488b4dc2a187d15a72990d640df2a8eef83/41a84d1d8029340f67148f65751a8fbefb08c455/README.yaml @@ -49,9 +49,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 439 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (83:9:9) bilayer at 310.15 K (CHARMM36, GROMACS 5.0, 200 ns) [NMRlipids simulation 439] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (83:9:9) bilayer at 310.15 + K (CHARMM36, GROMACS 5.0, 200 ns) [NMRlipids simulation 439] alternateName: 200POPC_9000SOL_21SOD_21CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 83 mol%), 21 CLA (9 mol%) and 21 SOD (9 mol%) at 310.15 K. Simulated with CHARMM36 in GROMACS 5.0 for 200 ns (53842 atoms). Deposited as NMRlipids Databank simulation 439 and available from https://doi.org/10.5281/zenodo.259392. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 83 mol%), 21 CLA (9 mol%) and 21 SOD (9 mol%) at 310.15 K. Simulated with CHARMM36 + in GROMACS 5.0 for 200 ns (53842 atoms). Deposited as NMRlipids Databank simulation + 439 and available from https://doi.org/10.5281/zenodo.259392. sameAs: https://doi.org/10.5281/zenodo.259392 datePublished: '2017-01-24' license: @@ -139,7 +143,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.259392 identifier: 10.5281/zenodo.259392 url: https://doi.org/10.5281/zenodo.259392 - name: Popc With Varying Amounts Of Cholesterol, 130 Mm Of Nacl. Charmm36 With Default Charmm Ions + name: Popc With Varying Amounts Of Cholesterol, 130 Mm Of Nacl. Charmm36 With + Default Charmm Ions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/79a/132/79a1323d322a607a3ba71f4188f6ee895a91655c/1d28447ecd68c98aefdba0cc4b09b10883b48594/README.yaml b/Simulations/79a/132/79a1323d322a607a3ba71f4188f6ee895a91655c/1d28447ecd68c98aefdba0cc4b09b10883b48594/README.yaml index b7a33b28d9..8050bb1968 100644 --- a/Simulations/79a/132/79a1323d322a607a3ba71f4188f6ee895a91655c/1d28447ecd68c98aefdba0cc4b09b10883b48594/README.yaml +++ b/Simulations/79a/132/79a1323d322a607a3ba71f4188f6ee895a91655c/1d28447ecd68c98aefdba0cc4b09b10883b48594/README.yaml @@ -50,9 +50,13 @@ SOFTWARE: gromacs DIR_WRK: /usr/home/bort/Databank ID: 398 bioschema_properties: - name: Molecular dynamics trajectory of a DDOPC/CHOL (90:10) bilayer at 310 K (CHARMM36, GROMACS, 1000 ns) [NMRlipids simulation 398] + name: Molecular dynamics trajectory of a DDOPC/CHOL (90:10) bilayer at 310 K (CHARMM36, + GROMACS, 1000 ns) [NMRlipids simulation 398] alternateName: 260DDOPC_28CHOL_11520SOL_310K - description: Molecular dynamics trajectory of a lipid bilayer of 260 DDOPC (1,2-didocosahexaenoyl-sn-glycero-3-phosphocholine, 90 mol%) and 28 CHOL (cholesterol, 10 mol%) at 310 K. Simulated with CHARMM36 in GROMACS for 1000 ns (73552 atoms). Deposited as NMRlipids Databank simulation 398 and available from https://doi.org/10.5281/zenodo.2653721. + description: Molecular dynamics trajectory of a lipid bilayer of 260 DDOPC (1,2-didocosahexaenoyl-sn-glycero-3-phosphocholine, + 90 mol%) and 28 CHOL (cholesterol, 10 mol%) at 310 K. Simulated with CHARMM36 + in GROMACS for 1000 ns (73552 atoms). Deposited as NMRlipids Databank simulation + 398 and available from https://doi.org/10.5281/zenodo.2653721. sameAs: https://doi.org/10.5281/zenodo.2653721 datePublished: '2019-04-29' license: @@ -141,7 +145,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.2653721 identifier: 10.5281/zenodo.2653721 url: https://doi.org/10.5281/zenodo.2653721 - name: Atomistic simulations of cholesterol in symmetric lipid bilayers with varying degrees of lipid chain unsaturation + name: Atomistic simulations of cholesterol in symmetric lipid bilayers with varying + degrees of lipid chain unsaturation publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/7a0/6cb/7a06cb48d1ab9c4f56a66006c487057cdcc2fb59/9d1fc1c4bd29ca523e55fefa8c3f652cd4b80ff7/README.yaml b/Simulations/7a0/6cb/7a06cb48d1ab9c4f56a66006c487057cdcc2fb59/9d1fc1c4bd29ca523e55fefa8c3f652cd4b80ff7/README.yaml index 7ad74d76ad..9535c67adb 100644 --- a/Simulations/7a0/6cb/7a06cb48d1ab9c4f56a66006c487057cdcc2fb59/9d1fc1c4bd29ca523e55fefa8c3f652cd4b80ff7/README.yaml +++ b/Simulations/7a0/6cb/7a06cb48d1ab9c4f56a66006c487057cdcc2fb59/9d1fc1c4bd29ca523e55fefa8c3f652cd4b80ff7/README.yaml @@ -56,9 +56,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 495 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPS/SOD (71:14:14) bilayer at 298 K (GROMOS-CKP, Berger/Chiu NH3 charges and PME, GROMACS, 100 ns) [NMRlipids simulation 495] + name: Molecular dynamics trajectory of a POPC/POPS/SOD (71:14:14) bilayer at 298 + K (GROMOS-CKP, Berger/Chiu NH3 charges and PME, GROMACS, 100 ns) [NMRlipids simulation + 495] alternateName: 110POPC_22POPS_4620SOL_22SOD_298K_GROMOS-CKP_v2 - description: Molecular dynamics trajectory of a lipid bilayer of 110 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 71 mol%), 22 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 14 mol%) and 22 SOD (14 mol%) at 298 K. Simulated with GROMOS-CKP, Berger/Chiu NH3 charges and PME in GROMACS for 100 ns (20812 atoms). Deposited as NMRlipids Databank simulation 495 and available from https://doi.org/10.5281/zenodo.1283331. + description: Molecular dynamics trajectory of a lipid bilayer of 110 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 71 mol%), 22 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 14 mol%) + and 22 SOD (14 mol%) at 298 K. Simulated with GROMOS-CKP, Berger/Chiu NH3 charges + and PME in GROMACS for 100 ns (20812 atoms). Deposited as NMRlipids Databank simulation + 495 and available from https://doi.org/10.5281/zenodo.1283331. sameAs: https://doi.org/10.5281/zenodo.1283331 datePublished: '2018-06-05' license: @@ -147,7 +153,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1283331 identifier: 10.5281/zenodo.1283331 url: https://doi.org/10.5281/zenodo.1283331 - name: Gromos-Ckp Pops/Popc Simulations (Versions 1 And 2) 298 K With Berger/Chiu Nh3 Charges And Pme + name: Gromos-Ckp Pops/Popc Simulations (Versions 1 And 2) 298 K With Berger/Chiu + Nh3 Charges And Pme publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/7a1/218/7a121890d1beef9377a0f5e257e5e0a69f49fdda/f02a0e4ef5381ad1d9752fd13c03d23194cd6299/README.yaml b/Simulations/7a1/218/7a121890d1beef9377a0f5e257e5e0a69f49fdda/f02a0e4ef5381ad1d9752fd13c03d23194cd6299/README.yaml index 68fd4eb185..3620efdbc8 100644 --- a/Simulations/7a1/218/7a121890d1beef9377a0f5e257e5e0a69f49fdda/f02a0e4ef5381ad1d9752fd13c03d23194cd6299/README.yaml +++ b/Simulations/7a1/218/7a121890d1beef9377a0f5e257e5e0a69f49fdda/f02a0e4ef5381ad1d9752fd13c03d23194cd6299/README.yaml @@ -60,9 +60,14 @@ EXPERIMENT: SAPI25: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POT/CLA/SAPI25 (66:23:8:4) bilayer at 298.15 K (CHARMM36m, GROMACS 2020.1, 1202 ns) [NMRlipids simulation 786] + name: Molecular dynamics trajectory of a POPC/POT/CLA/SAPI25 (66:23:8:4) bilayer + at 298.15 K (CHARMM36m, GROMACS 2020.1, 1202 ns) [NMRlipids simulation 786] alternateName: POPC_284_SAPI25_16_KCl_150mM_298.15K - description: Molecular dynamics trajectory of a lipid bilayer of 284 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 66 mol%), 98 POT (23 mol%), 34 CLA (8 mol%) and 16 SAPI25 (1-stearoyl-2-arachidonoyl-sn-phosphatidylinositol 4,5-biphosphate, 4 mol%) at 298.15 K. Simulated with CHARMM36m in GROMACS 2020.1 for 1202 ns (80251 atoms). Deposited as NMRlipids Databank simulation 786 and available from https://doi.org/10.5281/zenodo.8370420. + description: Molecular dynamics trajectory of a lipid bilayer of 284 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 66 mol%), 98 POT (23 mol%), 34 CLA (8 mol%) and 16 SAPI25 (1-stearoyl-2-arachidonoyl-sn-phosphatidylinositol + 4,5-biphosphate, 4 mol%) at 298.15 K. Simulated with CHARMM36m in GROMACS 2020.1 + for 1202 ns (80251 atoms). Deposited as NMRlipids Databank simulation 786 and + available from https://doi.org/10.5281/zenodo.8370420. sameAs: https://doi.org/10.5281/zenodo.8370420 datePublished: '2023-09-22' license: diff --git a/Simulations/7a4/d3d/7a4d3d37ebd3b62978f03dc8e00dae4e8760d653/b645338a2b8b2dde02f51db00ff96dd6d204dc8e/README.yaml b/Simulations/7a4/d3d/7a4d3d37ebd3b62978f03dc8e00dae4e8760d653/b645338a2b8b2dde02f51db00ff96dd6d204dc8e/README.yaml index 0b276c81ff..123277d9de 100644 --- a/Simulations/7a4/d3d/7a4d3d37ebd3b62978f03dc8e00dae4e8760d653/b645338a2b8b2dde02f51db00ff96dd6d204dc8e/README.yaml +++ b/Simulations/7a4/d3d/7a4d3d37ebd3b62978f03dc8e00dae4e8760d653/b645338a2b8b2dde02f51db00ff96dd6d204dc8e/README.yaml @@ -50,9 +50,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 506 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (70:30) bilayer at 303.15 K (CHARMM36, GROMACS 5.1.2, 100 ns) [NMRlipids simulation 506] + name: Molecular dynamics trajectory of a POPC/CHOL (70:30) bilayer at 303.15 K (CHARMM36, + GROMACS 5.1.2, 100 ns) [NMRlipids simulation 506] alternateName: 84POPC_4800SOL_36CHOL_303.84K - description: Molecular dynamics trajectory of a lipid bilayer of 84 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 70 mol%) and 36 CHOL (cholesterol, 30 mol%) at 303.15 K. Simulated with CHARMM36 in GROMACS 5.1.2 for 100 ns (28320 atoms). Deposited as NMRlipids Databank simulation 506 and available from https://doi.org/10.5281/zenodo.209362. + description: Molecular dynamics trajectory of a lipid bilayer of 84 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 70 mol%) and 36 CHOL (cholesterol, 30 mol%) at 303.15 K. Simulated with CHARMM36 + in GROMACS 5.1.2 for 100 ns (28320 atoms). Deposited as NMRlipids Databank simulation + 506 and available from https://doi.org/10.5281/zenodo.209362. sameAs: https://doi.org/10.5281/zenodo.209362 datePublished: '2016-12-19' license: @@ -142,7 +146,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.209362 identifier: 10.5281/zenodo.209362 url: https://doi.org/10.5281/zenodo.209362 - name: Popc/Cholesterol (70:30) Lipid Membrane, 303K, Charmm36 Force Field, Simulation Files And 100 Ns Trajectory For Gromacs Simulation Engine V5.1.2 + name: Popc/Cholesterol (70:30) Lipid Membrane, 303K, Charmm36 Force Field, Simulation + Files And 100 Ns Trajectory For Gromacs Simulation Engine V5.1.2 publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/7a7/591/7a7591afc8a748eb8a19807401ef6d297f36c202/de3454b64be6b9c9d2dc17d873ca1cfbca1c6766/README.yaml b/Simulations/7a7/591/7a7591afc8a748eb8a19807401ef6d297f36c202/de3454b64be6b9c9d2dc17d873ca1cfbca1c6766/README.yaml index dfa8c38399..db0c5ba942 100644 --- a/Simulations/7a7/591/7a7591afc8a748eb8a19807401ef6d297f36c202/de3454b64be6b9c9d2dc17d873ca1cfbca1c6766/README.yaml +++ b/Simulations/7a7/591/7a7591afc8a748eb8a19807401ef6d297f36c202/de3454b64be6b9c9d2dc17d873ca1cfbca1c6766/README.yaml @@ -41,9 +41,12 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 522 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 310.15 K (ECC-CHARMM36, GROMACS 5.1.4, 367 ns) [NMRlipids simulation 522] + name: Molecular dynamics trajectory of a POPC bilayer at 310.15 K (ECC-CHARMM36, + GROMACS 5.1.4, 367 ns) [NMRlipids simulation 522] alternateName: 200POPC_9000SOL_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 310.15 K. Simulated with ECC-CHARMM36 in GROMACS 5.1.4 for 367 ns (53800 atoms). Deposited as NMRlipids Databank simulation 522 and available from https://doi.org/10.5281/zenodo.2562080. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 310.15 K. Simulated with ECC-CHARMM36 in GROMACS 5.1.4 for 367 ns (53800 atoms). + Deposited as NMRlipids Databank simulation 522 and available from https://doi.org/10.5281/zenodo.2562080. sameAs: https://doi.org/10.5281/zenodo.2562080 datePublished: '2019-02-11' license: @@ -129,7 +132,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.2562080 identifier: 10.5281/zenodo.2562080 url: https://doi.org/10.5281/zenodo.2562080 - name: Simulation data for ECC-CHARMM36 POPC bilayer, 100 lipids/leaflet, 310K, GROMACS 5.1.4 + name: Simulation data for ECC-CHARMM36 POPC bilayer, 100 lipids/leaflet, 310K, + GROMACS 5.1.4 publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/7ab/2b4/7ab2b45dcff6f8ff34f5f26d8d15fb94f7cf3393/1d42d856ac5622426ba19d7a73030b1a749f817a/README.yaml b/Simulations/7ab/2b4/7ab2b45dcff6f8ff34f5f26d8d15fb94f7cf3393/1d42d856ac5622426ba19d7a73030b1a749f817a/README.yaml index 7adc6b4f3d..35009c0d19 100644 --- a/Simulations/7ab/2b4/7ab2b45dcff6f8ff34f5f26d8d15fb94f7cf3393/1d42d856ac5622426ba19d7a73030b1a749f817a/README.yaml +++ b/Simulations/7ab/2b4/7ab2b45dcff6f8ff34f5f26d8d15fb94f7cf3393/1d42d856ac5622426ba19d7a73030b1a749f817a/README.yaml @@ -60,9 +60,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 581 bioschema_properties: - name: Molecular dynamics trajectory of a CLA/DMPC/DMTAP (33:33:33) bilayer at 323 K (Berger with DMTAP modification by Gurtovenko et al., GROMACS 3.x, 150 ns) [NMRlipids simulation 581] + name: Molecular dynamics trajectory of a CLA/DMPC/DMTAP (33:33:33) bilayer at 323 + K (Berger with DMTAP modification by Gurtovenko et al., GROMACS 3.x, 150 ns) [NMRlipids + simulation 581] alternateName: 64DMPC_64DMTAP_64CLA_5336SOL_323K - description: Molecular dynamics trajectory of a lipid bilayer of 64 CLA (33 mol%), 64 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine, 33 mol%) and 64 DMTAP (1,2-dimyristoyl-3-trimethylammonium-propane, 33 mol%) at 323 K. Simulated with Berger with DMTAP modification by Gurtovenko et al. in GROMACS 3.x for 150 ns (21512 atoms). Deposited as NMRlipids Databank simulation 581 and available from https://doi.org/10.5281/zenodo.51748. + description: Molecular dynamics trajectory of a lipid bilayer of 64 CLA (33 mol%), + 64 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine, 33 mol%) and 64 DMTAP (1,2-dimyristoyl-3-trimethylammonium-propane, + 33 mol%) at 323 K. Simulated with Berger with DMTAP modification by Gurtovenko + et al. in GROMACS 3.x for 150 ns (21512 atoms). Deposited as NMRlipids Databank + simulation 581 and available from https://doi.org/10.5281/zenodo.51748. sameAs: https://doi.org/10.5281/zenodo.51748 datePublished: '2016-05-20' license: @@ -159,7 +165,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.51748 identifier: 10.5281/zenodo.51748 url: https://doi.org/10.5281/zenodo.51748 - name: 'Molecular dynamics simulation trajectory of a cationic lipid bilayer: 50/50 mol% DMTAP/DMPC' + name: 'Molecular dynamics simulation trajectory of a cationic lipid bilayer: 50/50 + mol% DMTAP/DMPC' publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/7af/288/7af288083118561ffb3a586b361e49f0a5a751af/fb9a5ab02b984b80b916d1fc7d7fc2363d08e800/README.yaml b/Simulations/7af/288/7af288083118561ffb3a586b361e49f0a5a751af/fb9a5ab02b984b80b916d1fc7d7fc2363d08e800/README.yaml index 8c97efe203..7ff9c9b016 100644 --- a/Simulations/7af/288/7af288083118561ffb3a586b361e49f0a5a751af/fb9a5ab02b984b80b916d1fc7d7fc2363d08e800/README.yaml +++ b/Simulations/7af/288/7af288083118561ffb3a586b361e49f0a5a751af/fb9a5ab02b984b80b916d1fc7d7fc2363d08e800/README.yaml @@ -43,9 +43,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 194 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 310 K (Slipids, GROMACS 2018.3, 100 ns) [NMRlipids simulation 194] + name: Molecular dynamics trajectory of a POPC bilayer at 310 K (Slipids, GROMACS + 2018.3, 100 ns) [NMRlipids simulation 194] alternateName: 500POPC_25000SOL_310K - description: Molecular dynamics trajectory of a lipid bilayer of 500 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 310 K. Simulated with Slipids in GROMACS 2018.3 for 100 ns (142000 atoms). Deposited as NMRlipids Databank simulation 194 and available from https://doi.org/10.5281/zenodo.3235552. + description: Molecular dynamics trajectory of a lipid bilayer of 500 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 310 K. Simulated with Slipids in GROMACS 2018.3 for 100 ns (142000 atoms). + Deposited as NMRlipids Databank simulation 194 and available from https://doi.org/10.5281/zenodo.3235552. sameAs: https://doi.org/10.5281/zenodo.3235552 datePublished: '2019-05-30' license: diff --git a/Simulations/7b5/dac/7b5dacbf8d86861371b86fcfb541daaaa1b08756/f055c6e1ecf88e3e920f5dc29f0527f31e114c82/README.yaml b/Simulations/7b5/dac/7b5dacbf8d86861371b86fcfb541daaaa1b08756/f055c6e1ecf88e3e920f5dc29f0527f31e114c82/README.yaml index f6d4ecb2b5..7298cf5a2a 100644 --- a/Simulations/7b5/dac/7b5dacbf8d86861371b86fcfb541daaaa1b08756/f055c6e1ecf88e3e920f5dc29f0527f31e114c82/README.yaml +++ b/Simulations/7b5/dac/7b5dacbf8d86861371b86fcfb541daaaa1b08756/f055c6e1ecf88e3e920f5dc29f0527f31e114c82/README.yaml @@ -45,9 +45,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 568 bioschema_properties: - name: Molecular dynamics trajectory of a POPG/SOD (50:50) bilayer at 310 K (CHARMM36, GROMACS 2018.3, 100 ns) [NMRlipids simulation 568] + name: Molecular dynamics trajectory of a POPG/SOD (50:50) bilayer at 310 K (CHARMM36, + GROMACS 2018.3, 100 ns) [NMRlipids simulation 568] alternateName: 500POPG_25000SOL_500SOD_310K - description: Molecular dynamics trajectory of a lipid bilayer of 500 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 50 mol%) and 500 SOD (50 mol%) at 310 K. Simulated with CHARMM36 in GROMACS 2018.3 for 100 ns (139000 atoms). Deposited as NMRlipids Databank simulation 568 and available from https://doi.org/10.5281/zenodo.3237463. + description: Molecular dynamics trajectory of a lipid bilayer of 500 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, + 50 mol%) and 500 SOD (50 mol%) at 310 K. Simulated with CHARMM36 in GROMACS 2018.3 + for 100 ns (139000 atoms). Deposited as NMRlipids Databank simulation 568 and + available from https://doi.org/10.5281/zenodo.3237463. sameAs: https://doi.org/10.5281/zenodo.3237463 datePublished: '2019-06-03' license: diff --git a/Simulations/7b7/c2e/7b7c2e970801123e53619b9d50ce3d03bbc9f8db/d53857373c400e0ff9f989bca5c8a136c764f71e/README.yaml b/Simulations/7b7/c2e/7b7c2e970801123e53619b9d50ce3d03bbc9f8db/d53857373c400e0ff9f989bca5c8a136c764f71e/README.yaml index f6bd640fab..f49262c840 100644 --- a/Simulations/7b7/c2e/7b7c2e970801123e53619b9d50ce3d03bbc9f8db/d53857373c400e0ff9f989bca5c8a136c764f71e/README.yaml +++ b/Simulations/7b7/c2e/7b7c2e970801123e53619b9d50ce3d03bbc9f8db/d53857373c400e0ff9f989bca5c8a136c764f71e/README.yaml @@ -50,9 +50,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 872 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (56:22:22) bilayer at 300 K (CHARMM36, GROMACS 2019.5, 440 ns) [NMRlipids simulation 872] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (56:22:22) bilayer at 300 + K (CHARMM36, GROMACS 2019.5, 440 ns) [NMRlipids simulation 872] alternateName: POPC, 44 w/l, 300 K, 0.5 M NaCl - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 56 mol%), 80 CLA (22 mol%) and 80 SOD (22 mol%) at 300 K. Simulated with CHARMM36 in GROMACS 2019.5 for 440 ns (53600 atoms). Deposited as NMRlipids Databank simulation 872 and available from https://doi.org/10.5281/zenodo.6342522. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 56 mol%), 80 CLA (22 mol%) and 80 SOD (22 mol%) at 300 K. Simulated with CHARMM36 + in GROMACS 2019.5 for 440 ns (53600 atoms). Deposited as NMRlipids Databank simulation + 872 and available from https://doi.org/10.5281/zenodo.6342522. sameAs: https://doi.org/10.5281/zenodo.6342522 datePublished: '2022-03-10' license: diff --git a/Simulations/7b9/b36/7b9b364499f2cc70448948aad5670f56bff013f3/a82513d93469063b8bab6b622043362f6af502f2/README.yaml b/Simulations/7b9/b36/7b9b364499f2cc70448948aad5670f56bff013f3/a82513d93469063b8bab6b622043362f6af502f2/README.yaml index 560198092f..014cc33dda 100644 --- a/Simulations/7b9/b36/7b9b364499f2cc70448948aad5670f56bff013f3/a82513d93469063b8bab6b622043362f6af502f2/README.yaml +++ b/Simulations/7b9/b36/7b9b364499f2cc70448948aad5670f56bff013f3/a82513d93469063b8bab6b622043362f6af502f2/README.yaml @@ -33,9 +33,12 @@ EXPERIMENT: DPPC: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a DPPC bilayer at 333 K (CHARMM36, GROMACS, 100 ns) [NMRlipids simulation 884] + name: Molecular dynamics trajectory of a DPPC bilayer at 333 K (CHARMM36, GROMACS, + 100 ns) [NMRlipids simulation 884] alternateName: DPPC - description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) at 333 K. Simulated with CHARMM36 in GROMACS for 100 ns (13347 atoms). Deposited as NMRlipids Databank simulation 884 and available from https://doi.org/10.5281/zenodo.7572990. + description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) + at 333 K. Simulated with CHARMM36 in GROMACS for 100 ns (13347 atoms). Deposited + as NMRlipids Databank simulation 884 and available from https://doi.org/10.5281/zenodo.7572990. sameAs: https://doi.org/10.5281/zenodo.7572990 datePublished: '2023-01-26' license: @@ -125,7 +128,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.7572990 identifier: 10.5281/zenodo.7572990 url: https://doi.org/10.5281/zenodo.7572990 - name: 'MD simulation input files and results for ,,Atomistic MD simulations of n-alkanes in a phospholipid bilayer: CHARMM36 versus Slipids"' + name: 'MD simulation input files and results for ,,Atomistic MD simulations of + n-alkanes in a phospholipid bilayer: CHARMM36 versus Slipids"' publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/7c4/79b/7c479b069055ffc45de18570df934c82c9bb5548/d1f61a7076c6cd4d1a43bcb612e0a3cd95b845ee/README.yaml b/Simulations/7c4/79b/7c479b069055ffc45de18570df934c82c9bb5548/d1f61a7076c6cd4d1a43bcb612e0a3cd95b845ee/README.yaml index 7d0efb2791..6a5aa2b2a0 100644 --- a/Simulations/7c4/79b/7c479b069055ffc45de18570df934c82c9bb5548/d1f61a7076c6cd4d1a43bcb612e0a3cd95b845ee/README.yaml +++ b/Simulations/7c4/79b/7c479b069055ffc45de18570df934c82c9bb5548/d1f61a7076c6cd4d1a43bcb612e0a3cd95b845ee/README.yaml @@ -42,9 +42,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 656 bioschema_properties: - name: Molecular dynamics trajectory of a SOPC bilayer at 298.15 K (CHARMM36, GROMACS 2021, 1001 ns) [NMRlipids simulation 656] + name: Molecular dynamics trajectory of a SOPC bilayer at 298.15 K (CHARMM36, GROMACS + 2021, 1001 ns) [NMRlipids simulation 656] alternateName: SOPC_M - description: Molecular dynamics trajectory of a lipid bilayer of 256 SOPC (1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 298.15 K. Simulated with CHARMM36 in GROMACS 2021 for 1001 ns (74240 atoms). Deposited as NMRlipids Databank simulation 656 and available from https://doi.org/10.5281/zenodo.7103807. + description: Molecular dynamics trajectory of a lipid bilayer of 256 SOPC (1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 298.15 K. Simulated with CHARMM36 in GROMACS 2021 for 1001 ns (74240 atoms). + Deposited as NMRlipids Databank simulation 656 and available from https://doi.org/10.5281/zenodo.7103807. sameAs: https://doi.org/10.5281/zenodo.7103807 datePublished: '2022-09-22' license: diff --git a/Simulations/7cb/7a3/7cb7a3281b5e79d8e0328d82cdebbcc11f1bab2a/f89b798e078bcc3f9793b20176dbe25ae42778ad/README.yaml b/Simulations/7cb/7a3/7cb7a3281b5e79d8e0328d82cdebbcc11f1bab2a/f89b798e078bcc3f9793b20176dbe25ae42778ad/README.yaml index 1203aa770f..0e105dcc64 100644 --- a/Simulations/7cb/7a3/7cb7a3281b5e79d8e0328d82cdebbcc11f1bab2a/f89b798e078bcc3f9793b20176dbe25ae42778ad/README.yaml +++ b/Simulations/7cb/7a3/7cb7a3281b5e79d8e0328d82cdebbcc11f1bab2a/f89b798e078bcc3f9793b20176dbe25ae42778ad/README.yaml @@ -64,9 +64,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 185 bioschema_properties: - name: Molecular dynamics trajectory of a DMPC/CLA/SOD/DMTAP (38:31:28:3) bilayer at 323 K (Berger with DMTAP modification by Gurtovenko et al., GROMACS 3.x, 230 ns) [NMRlipids simulation 185] + name: Molecular dynamics trajectory of a DMPC/CLA/SOD/DMTAP (38:31:28:3) bilayer + at 323 K (Berger with DMTAP modification by Gurtovenko et al., GROMACS 3.x, 230 + ns) [NMRlipids simulation 185] alternateName: 120DMPC_8DMTAP_89SOD_97CLA_4921SOL_323K - description: Molecular dynamics trajectory of a lipid bilayer of 120 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine, 38 mol%), 97 CLA (31 mol%), 89 SOD (28 mol%) and 8 DMTAP (1,2-dimyristoyl-3-trimethylammonium-propane, 3 mol%) at 323 K. Simulated with Berger with DMTAP modification by Gurtovenko et al. in GROMACS 3.x for 230 ns (20781 atoms). Deposited as NMRlipids Databank simulation 185 and available from https://doi.org/10.5281/zenodo.53222. + description: Molecular dynamics trajectory of a lipid bilayer of 120 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine, + 38 mol%), 97 CLA (31 mol%), 89 SOD (28 mol%) and 8 DMTAP (1,2-dimyristoyl-3-trimethylammonium-propane, + 3 mol%) at 323 K. Simulated with Berger with DMTAP modification by Gurtovenko + et al. in GROMACS 3.x for 230 ns (20781 atoms). Deposited as NMRlipids Databank + simulation 185 and available from https://doi.org/10.5281/zenodo.53222. sameAs: https://doi.org/10.5281/zenodo.53222 datePublished: '2016-05-28' license: @@ -165,7 +171,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.53222 identifier: 10.5281/zenodo.53222 url: https://doi.org/10.5281/zenodo.53222 - name: 'Molecular dynamics simulation trajectory of a cationic lipid bilayer: 6/94 mol% DMTAP/DMPC in 1.0 M NaCl' + name: 'Molecular dynamics simulation trajectory of a cationic lipid bilayer: 6/94 + mol% DMTAP/DMPC in 1.0 M NaCl' publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/7ce/652/7ce652f1f82b5762795ce7c3f3f8f5bf97019160/cd2aff34199a5e8ef90f52a1ec22049b4269ea25/README.yaml b/Simulations/7ce/652/7ce652f1f82b5762795ce7c3f3f8f5bf97019160/cd2aff34199a5e8ef90f52a1ec22049b4269ea25/README.yaml index b684e41e3b..8acc0ee84b 100644 --- a/Simulations/7ce/652/7ce652f1f82b5762795ce7c3f3f8f5bf97019160/cd2aff34199a5e8ef90f52a1ec22049b4269ea25/README.yaml +++ b/Simulations/7ce/652/7ce652f1f82b5762795ce7c3f3f8f5bf97019160/cd2aff34199a5e8ef90f52a1ec22049b4269ea25/README.yaml @@ -54,9 +54,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 161 bioschema_properties: - name: Molecular dynamics trajectory of a POPG/SOD/POPE (43:43:14) bilayer at 310 K (Slipids, GROMACS 2018.3, 100 ns) [NMRlipids simulation 161] + name: Molecular dynamics trajectory of a POPG/SOD/POPE (43:43:14) bilayer at 310 + K (Slipids, GROMACS 2018.3, 100 ns) [NMRlipids simulation 161] alternateName: 374POPG_126POPE_25000SOL_374SOD_310K - description: Molecular dynamics trajectory of a lipid bilayer of 374 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 43 mol%), 374 SOD (43 mol%) and 126 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 14 mol%) at 310 K. Simulated with Slipids in GROMACS 2018.3 for 100 ns (138622 atoms). Deposited as NMRlipids Databank simulation 161 and available from https://doi.org/10.5281/zenodo.3240403. + description: Molecular dynamics trajectory of a lipid bilayer of 374 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, + 43 mol%), 374 SOD (43 mol%) and 126 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, + 14 mol%) at 310 K. Simulated with Slipids in GROMACS 2018.3 for 100 ns (138622 + atoms). Deposited as NMRlipids Databank simulation 161 and available from https://doi.org/10.5281/zenodo.3240403. sameAs: https://doi.org/10.5281/zenodo.3240403 datePublished: '2019-06-06' license: diff --git a/Simulations/7cf/9df/7cf9df0cc6fe319d93e3f5635b2c6b517513cbf5/b1e8bdfc572caaf640f503bff2726ed0a1a793a3/README.yaml b/Simulations/7cf/9df/7cf9df0cc6fe319d93e3f5635b2c6b517513cbf5/b1e8bdfc572caaf640f503bff2726ed0a1a793a3/README.yaml index a7508ca49a..d75665b505 100644 --- a/Simulations/7cf/9df/7cf9df0cc6fe319d93e3f5635b2c6b517513cbf5/b1e8bdfc572caaf640f503bff2726ed0a1a793a3/README.yaml +++ b/Simulations/7cf/9df/7cf9df0cc6fe319d93e3f5635b2c6b517513cbf5/b1e8bdfc572caaf640f503bff2726ed0a1a793a3/README.yaml @@ -44,9 +44,14 @@ SOFTWARE: gromacs DIR_WRK: /usr/home/bort/Databank ID: 144 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 303 K (CHARMM36 (center of mass removed independently for upper leaflet, lower leaflet and water+ions), GROMACS 5.0.4, 500 ns) [NMRlipids simulation 144] + name: Molecular dynamics trajectory of a POPC bilayer at 303 K (CHARMM36 (center + of mass removed independently for upper leaflet, lower leaflet and water+ions), + GROMACS 5.0.4, 500 ns) [NMRlipids simulation 144] alternateName: 72POPC_2239SOL_303K_rmcomm_leaflets - description: Molecular dynamics trajectory of a lipid bilayer of 72 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 303 K. Simulated with CHARMM36 (center of mass removed independently for upper leaflet, lower leaflet and water+ions) in GROMACS 5.0.4 for 500 ns (16365 atoms). Deposited as NMRlipids Databank simulation 144 and available from https://doi.org/10.5281/zenodo.1009607. + description: Molecular dynamics trajectory of a lipid bilayer of 72 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 303 K. Simulated with CHARMM36 (center of mass removed independently for upper + leaflet, lower leaflet and water+ions) in GROMACS 5.0.4 for 500 ns (16365 atoms). + Deposited as NMRlipids Databank simulation 144 and available from https://doi.org/10.5281/zenodo.1009607. sameAs: https://doi.org/10.5281/zenodo.1009607 datePublished: '2017-10-12' license: @@ -99,7 +104,8 @@ bioschema_properties: inDefinedTermSet: http://edamontology.org url: http://edamontology.org/operation_2476 - Molecular dynamics simulation (gromacs 5.0.4) - - CHARMM36 (center of mass removed independently for upper leaflet, lower leaflet and water+ions) force field + - CHARMM36 (center of mass removed independently for upper leaflet, lower leaflet + and water+ions) force field variableMeasured: - '@type': PropertyValue name: area per lipid @@ -141,7 +147,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1009607 identifier: 10.5281/zenodo.1009607 url: https://doi.org/10.5281/zenodo.1009607 - name: Set Simulations Small Pure Bilayers (72 Lipids) Using Charmm36 Ff In Gromacs (Dppc, Popc) + name: Set Simulations Small Pure Bilayers (72 Lipids) Using Charmm36 Ff In Gromacs + (Dppc, Popc) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/7d1/181/7d1181a267a9a015e74f3f24594c0dc0ba0fce6a/09813ab2ccb777e53961f11f35c5f8398981bc98/README.yaml b/Simulations/7d1/181/7d1181a267a9a015e74f3f24594c0dc0ba0fce6a/09813ab2ccb777e53961f11f35c5f8398981bc98/README.yaml index 1ba8f76549..c7336111f4 100644 --- a/Simulations/7d1/181/7d1181a267a9a015e74f3f24594c0dc0ba0fce6a/09813ab2ccb777e53961f11f35c5f8398981bc98/README.yaml +++ b/Simulations/7d1/181/7d1181a267a9a015e74f3f24594c0dc0ba0fce6a/09813ab2ccb777e53961f11f35c5f8398981bc98/README.yaml @@ -45,9 +45,12 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/1 ID: 657 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 298.15 K (Lipid17, GROMACS 2021, 1001 ns) [NMRlipids simulation 657] + name: Molecular dynamics trajectory of a POPC bilayer at 298.15 K (Lipid17, GROMACS + 2021, 1001 ns) [NMRlipids simulation 657] alternateName: Lipid17_POPC_M - description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 298.15 K. Simulated with Lipid17 in GROMACS 2021 for 1001 ns (72704 atoms). Deposited as NMRlipids Databank simulation 657 and available from https://doi.org/10.5281/zenodo.6992065. + description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 298.15 K. Simulated with Lipid17 in GROMACS 2021 for 1001 ns (72704 atoms). + Deposited as NMRlipids Databank simulation 657 and available from https://doi.org/10.5281/zenodo.6992065. sameAs: https://doi.org/10.5281/zenodo.6992065 datePublished: '2022-08-15' license: diff --git a/Simulations/7d7/c42/7d7c42a7ef3419560ab1dabb52161728d62f2a7f/a5bb1d1fd6165db5e9784b8e3f1b0a25381ba680/README.yaml b/Simulations/7d7/c42/7d7c42a7ef3419560ab1dabb52161728d62f2a7f/a5bb1d1fd6165db5e9784b8e3f1b0a25381ba680/README.yaml index cf4bf6557b..858841486c 100644 --- a/Simulations/7d7/c42/7d7c42a7ef3419560ab1dabb52161728d62f2a7f/a5bb1d1fd6165db5e9784b8e3f1b0a25381ba680/README.yaml +++ b/Simulations/7d7/c42/7d7c42a7ef3419560ab1dabb52161728d62f2a7f/a5bb1d1fd6165db5e9784b8e3f1b0a25381ba680/README.yaml @@ -45,9 +45,12 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/1 ID: 658 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 298.15 K (MacRog, GROMACS 2021, 1001 ns) [NMRlipids simulation 658] + name: Molecular dynamics trajectory of a POPC bilayer at 298.15 K (MacRog, GROMACS + 2021, 1001 ns) [NMRlipids simulation 658] alternateName: MacRog_POPC_L - description: Molecular dynamics trajectory of a lipid bilayer of 1024 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 298.15 K. Simulated with MacRog in GROMACS 2021 for 1001 ns (290816 atoms). Deposited as NMRlipids Databank simulation 658 and available from https://doi.org/10.5281/zenodo.7061800. + description: Molecular dynamics trajectory of a lipid bilayer of 1024 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 298.15 K. Simulated with MacRog in GROMACS 2021 for 1001 ns (290816 atoms). + Deposited as NMRlipids Databank simulation 658 and available from https://doi.org/10.5281/zenodo.7061800. sameAs: https://doi.org/10.5281/zenodo.7061800 datePublished: '2022-09-08' license: diff --git a/Simulations/7e0/4cc/7e04cc61200fa210db3f847a93192fbc0311656c/4458ea38d2035775d13e1ba6b7cf84ba7a17cdfb/README.yaml b/Simulations/7e0/4cc/7e04cc61200fa210db3f847a93192fbc0311656c/4458ea38d2035775d13e1ba6b7cf84ba7a17cdfb/README.yaml index fab025c7e9..768612e4dc 100644 --- a/Simulations/7e0/4cc/7e04cc61200fa210db3f847a93192fbc0311656c/4458ea38d2035775d13e1ba6b7cf84ba7a17cdfb/README.yaml +++ b/Simulations/7e0/4cc/7e04cc61200fa210db3f847a93192fbc0311656c/4458ea38d2035775d13e1ba6b7cf84ba7a17cdfb/README.yaml @@ -49,9 +49,14 @@ EXPERIMENT: POPE: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a SOD/POPE/TOCL (50:25:25) bilayer at 310 K (Charmm36, GROMACS, 530 ns) [NMRlipids simulation 772] + name: Molecular dynamics trajectory of a SOD/POPE/TOCL (50:25:25) bilayer at 310 + K (Charmm36, GROMACS, 530 ns) [NMRlipids simulation 772] alternateName: POPC/TOCL mixture - description: Molecular dynamics trajectory of a lipid bilayer of 120 SOD (50 mol%), 60 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 25 mol%) and 60 TOCL (1’,3’-Bis[1,2-dioleoyl-sn-glycero-3-phospho]-glycerol, 25 mol%) at 310 K. Simulated with Charmm36 in GROMACS for 530 ns (58500 atoms). Deposited as NMRlipids Databank simulation 772 and available from https://doi.org/10.5281/zenodo.13984201. + description: Molecular dynamics trajectory of a lipid bilayer of 120 SOD (50 mol%), + 60 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 25 mol%) and 60 + TOCL (1’,3’-Bis[1,2-dioleoyl-sn-glycero-3-phospho]-glycerol, 25 mol%) at 310 K. + Simulated with Charmm36 in GROMACS for 530 ns (58500 atoms). Deposited as NMRlipids + Databank simulation 772 and available from https://doi.org/10.5281/zenodo.13984201. sameAs: https://doi.org/10.5281/zenodo.13984201 datePublished: '2023-09-29' license: diff --git a/Simulations/7e2/66a/7e266a6989c04c46a79a2f444b521c595053c4e1/7de7367161b8ffa3b3388f6b5f61825aacf8a360/README.yaml b/Simulations/7e2/66a/7e266a6989c04c46a79a2f444b521c595053c4e1/7de7367161b8ffa3b3388f6b5f61825aacf8a360/README.yaml index 389fa4df40..d81b8c2e92 100644 --- a/Simulations/7e2/66a/7e266a6989c04c46a79a2f444b521c595053c4e1/7de7367161b8ffa3b3388f6b5f61825aacf8a360/README.yaml +++ b/Simulations/7e2/66a/7e266a6989c04c46a79a2f444b521c595053c4e1/7de7367161b8ffa3b3388f6b5f61825aacf8a360/README.yaml @@ -48,9 +48,13 @@ EXPERIMENT: - 10.1039/C4SM00066H/3 ID: 480 bioschema_properties: - name: Molecular dynamics trajectory of a POPS/SOD (50:50) bilayer at 298 K (Berger, GROMACS, 100 ns) [NMRlipids simulation 480] + name: Molecular dynamics trajectory of a POPS/SOD (50:50) bilayer at 298 K (Berger, + GROMACS, 100 ns) [NMRlipids simulation 480] alternateName: POPS_298K_Berger - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 50 mol%) and 128 SOD (50 mol%) at 298 K. Simulated with Berger in GROMACS for 100 ns (20608 atoms). Deposited as NMRlipids Databank simulation 480 and available from https://doi.org/10.5281/zenodo.1129425. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, + 50 mol%) and 128 SOD (50 mol%) at 298 K. Simulated with Berger in GROMACS for + 100 ns (20608 atoms). Deposited as NMRlipids Databank simulation 480 and available + from https://doi.org/10.5281/zenodo.1129425. sameAs: https://doi.org/10.5281/zenodo.1129425 datePublished: '2017-12-24' license: diff --git a/Simulations/7e3/aee/7e3aee7e91ea20ef3030b626b67e3438996cd9f1/703646f01aa17d6346f951f8e2b1954b6a395591/README.yaml b/Simulations/7e3/aee/7e3aee7e91ea20ef3030b626b67e3438996cd9f1/703646f01aa17d6346f951f8e2b1954b6a395591/README.yaml index bfc835c114..0ec5979261 100644 --- a/Simulations/7e3/aee/7e3aee7e91ea20ef3030b626b67e3438996cd9f1/703646f01aa17d6346f951f8e2b1954b6a395591/README.yaml +++ b/Simulations/7e3/aee/7e3aee7e91ea20ef3030b626b67e3438996cd9f1/703646f01aa17d6346f951f8e2b1954b6a395591/README.yaml @@ -44,9 +44,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 516 bioschema_properties: - name: Molecular dynamics trajectory of a POPE bilayer at 303 K (Berger, GROMACS 4.0.7, 100 ns) [NMRlipids simulation 516] + name: Molecular dynamics trajectory of a POPE bilayer at 303 K (Berger, GROMACS + 4.0.7, 100 ns) [NMRlipids simulation 516] alternateName: 128POPE_3552SOL_303K_Berger_v1 - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) at 303 K. Simulated with Berger in GROMACS 4.0.7 for 100 ns (17312 atoms). Deposited as NMRlipids Databank simulation 516 and available from https://doi.org/10.5281/zenodo.1293891. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) + at 303 K. Simulated with Berger in GROMACS 4.0.7 for 100 ns (17312 atoms). Deposited + as NMRlipids Databank simulation 516 and available from https://doi.org/10.5281/zenodo.1293891. sameAs: https://doi.org/10.5281/zenodo.1293891 datePublished: '2018-06-20' license: diff --git a/Simulations/7ec/129/7ec129e267d37f2980f994cec3d4fb0aad9b561d/7d1a9c4c77caecc96b68d512514fdf23f83159f9/README.yaml b/Simulations/7ec/129/7ec129e267d37f2980f994cec3d4fb0aad9b561d/7d1a9c4c77caecc96b68d512514fdf23f83159f9/README.yaml index d065f543b0..e8d2cfff34 100644 --- a/Simulations/7ec/129/7ec129e267d37f2980f994cec3d4fb0aad9b561d/7d1a9c4c77caecc96b68d512514fdf23f83159f9/README.yaml +++ b/Simulations/7ec/129/7ec129e267d37f2980f994cec3d4fb0aad9b561d/7d1a9c4c77caecc96b68d512514fdf23f83159f9/README.yaml @@ -49,9 +49,14 @@ SOFTWARE: gromacs DIR_WRK: /usr/home/bort/Databank ID: 134 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (45:27:27) bilayer at 310 K (Slipids for lipids, Kohagen for NaCl, GROMACS 4.6, 100 ns) [NMRlipids simulation 134] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (45:27:27) bilayer at 310 + K (Slipids for lipids, Kohagen for NaCl, GROMACS 4.6, 100 ns) [NMRlipids simulation + 134] alternateName: 200POPC_9000SOL_122SOD_122CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 45 mol%), 122 CLA (27 mol%) and 122 SOD (27 mol%) at 310 K. Simulated with Slipids for lipids, Kohagen for NaCl in GROMACS 4.6 for 100 ns (54044 atoms). Deposited as NMRlipids Databank simulation 134 and available from https://doi.org/10.5281/zenodo.35193. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 45 mol%), 122 CLA (27 mol%) and 122 SOD (27 mol%) at 310 K. Simulated with Slipids + for lipids, Kohagen for NaCl in GROMACS 4.6 for 100 ns (54044 atoms). Deposited + as NMRlipids Databank simulation 134 and available from https://doi.org/10.5281/zenodo.35193. sameAs: https://doi.org/10.5281/zenodo.35193 datePublished: '2015-12-11' license: diff --git a/Simulations/7ed/584/7ed5842b82361b5ff84b582e4825cf570584d454/21457e786373fa03e7142c38d38e4cc1ed9f7716/README.yaml b/Simulations/7ed/584/7ed5842b82361b5ff84b582e4825cf570584d454/21457e786373fa03e7142c38d38e4cc1ed9f7716/README.yaml index 54bc5fba7f..7bd620cb6e 100644 --- a/Simulations/7ed/584/7ed5842b82361b5ff84b582e4825cf570584d454/21457e786373fa03e7142c38d38e4cc1ed9f7716/README.yaml +++ b/Simulations/7ed/584/7ed5842b82361b5ff84b582e4825cf570584d454/21457e786373fa03e7142c38d38e4cc1ed9f7716/README.yaml @@ -44,9 +44,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 553 bioschema_properties: - name: Molecular dynamics trajectory of a DLIPC bilayer at 333.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 553] + name: Molecular dynamics trajectory of a DLIPC bilayer at 333.15 K (CHARMM36, GROMACS, + 1001 ns) [NMRlipids simulation 553] alternateName: 64DLIPC_3200SOL_333K - description: Molecular dynamics trajectory of a lipid bilayer of 64 DLIPC (1,2-dilinoleoyl-sn-glycero-3-phosphocholine) at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (18176 atoms). Deposited as NMRlipids Databank simulation 553 and available from https://doi.org/10.5281/zenodo.6943413. + description: Molecular dynamics trajectory of a lipid bilayer of 64 DLIPC (1,2-dilinoleoyl-sn-glycero-3-phosphocholine) + at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (18176 atoms). Deposited + as NMRlipids Databank simulation 553 and available from https://doi.org/10.5281/zenodo.6943413. sameAs: https://doi.org/10.5281/zenodo.6943413 datePublished: '2022-07-30' license: @@ -134,7 +137,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.6943413 identifier: 10.5281/zenodo.6943413 url: https://doi.org/10.5281/zenodo.6943413 - name: Simulations of different single-component bilayers, three different system sizes + name: Simulations of different single-component bilayers, three different system + sizes publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/7ee/0dd/7ee0dd27df2a8d15323124198450c6b1f1642702/7ee0dd27df2a8d15323124198450c6b1f1642702/README.yaml b/Simulations/7ee/0dd/7ee0dd27df2a8d15323124198450c6b1f1642702/7ee0dd27df2a8d15323124198450c6b1f1642702/README.yaml index fb18ea0dfb..770822ba5c 100644 --- a/Simulations/7ee/0dd/7ee0dd27df2a8d15323124198450c6b1f1642702/7ee0dd27df2a8d15323124198450c6b1f1642702/README.yaml +++ b/Simulations/7ee/0dd/7ee0dd27df2a8d15323124198450c6b1f1642702/7ee0dd27df2a8d15323124198450c6b1f1642702/README.yaml @@ -77,9 +77,16 @@ EXPERIMENT: CHOL: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPE/SOD/POPI/POPS/CHOL/CER180 (45:20:14:9:5:4:3) bilayer at 310 K (CHARMM36m, NAMD 2.14, 200 ns) [NMRlipids simulation 776] + name: Molecular dynamics trajectory of a POPC/POPE/SOD/POPI/POPS/CHOL/CER180 (45:20:14:9:5:4:3) + bilayer at 310 K (CHARMM36m, NAMD 2.14, 200 ns) [NMRlipids simulation 776] alternateName: 12CHOL,134POPC,60POPE,14POPS,26POPI,10CER180,10551SOL,40SOD - description: Molecular dynamics trajectory of a lipid bilayer of 134 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 45 mol%), 60 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 20 mol%), 40 SOD (14 mol%), 26 POPI (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoinositol, 9 mol%), 14 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 5 mol%), 12 CHOL (cholesterol, 4 mol%) and 10 CER180 (N-stearoyl-D-erythro-sphingosine, 3 mol%) at 310 K. Simulated with CHARMM36m in NAMD 2.14 for 200 ns (64487 atoms). Deposited as NMRlipids Databank simulation 776 and available from https://doi.org/10.5281/zenodo.8369427. + description: Molecular dynamics trajectory of a lipid bilayer of 134 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 45 mol%), 60 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 20 mol%), + 40 SOD (14 mol%), 26 POPI (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoinositol, + 9 mol%), 14 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 5 mol%), + 12 CHOL (cholesterol, 4 mol%) and 10 CER180 (N-stearoyl-D-erythro-sphingosine, + 3 mol%) at 310 K. Simulated with CHARMM36m in NAMD 2.14 for 200 ns (64487 atoms). + Deposited as NMRlipids Databank simulation 776 and available from https://doi.org/10.5281/zenodo.8369427. sameAs: https://doi.org/10.5281/zenodo.8369427 datePublished: '2023-09-18' license: diff --git a/Simulations/7f1/e99/7f1e99b0c92a51bd40e6664bdf40de523f9bdf73/6346ff94833ef129996b37a4e6ca64ded246b253/README.yaml b/Simulations/7f1/e99/7f1e99b0c92a51bd40e6664bdf40de523f9bdf73/6346ff94833ef129996b37a4e6ca64ded246b253/README.yaml index f63d81865f..e6464c11da 100644 --- a/Simulations/7f1/e99/7f1e99b0c92a51bd40e6664bdf40de523f9bdf73/6346ff94833ef129996b37a4e6ca64ded246b253/README.yaml +++ b/Simulations/7f1/e99/7f1e99b0c92a51bd40e6664bdf40de523f9bdf73/6346ff94833ef129996b37a4e6ca64ded246b253/README.yaml @@ -45,9 +45,12 @@ EXPERIMENT: - unpublished/nesterenkoDMPCbOG/1 FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a DMPC bilayer at 313.15 K (Charmm36, GROMACS 2022.5, 592 ns) [NMRlipids simulation 788] + name: Molecular dynamics trajectory of a DMPC bilayer at 313.15 K (Charmm36, GROMACS + 2022.5, 592 ns) [NMRlipids simulation 788] alternateName: DMPC(313K,rfz) - description: Molecular dynamics trajectory of a lipid bilayer of 64 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) at 313.15 K. Simulated with Charmm36 in GROMACS 2022.5 for 592 ns (17152 atoms). Deposited as NMRlipids Databank simulation 788 and available from https://doi.org/10.5281/zenodo.8431710. + description: Molecular dynamics trajectory of a lipid bilayer of 64 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) + at 313.15 K. Simulated with Charmm36 in GROMACS 2022.5 for 592 ns (17152 atoms). + Deposited as NMRlipids Databank simulation 788 and available from https://doi.org/10.5281/zenodo.8431710. sameAs: https://doi.org/10.5281/zenodo.8431710 datePublished: '2023-10-11' license: diff --git a/Simulations/7f1/f10/7f1f101895eed0e5b5344166106a5710ce18a82c/7f1f101895eed0e5b5344166106a5710ce18a82c/README.yaml b/Simulations/7f1/f10/7f1f101895eed0e5b5344166106a5710ce18a82c/7f1f101895eed0e5b5344166106a5710ce18a82c/README.yaml index 7ab04208b1..f59f7b8ebc 100644 --- a/Simulations/7f1/f10/7f1f101895eed0e5b5344166106a5710ce18a82c/7f1f101895eed0e5b5344166106a5710ce18a82c/README.yaml +++ b/Simulations/7f1/f10/7f1f101895eed0e5b5344166106a5710ce18a82c/7f1f101895eed0e5b5344166106a5710ce18a82c/README.yaml @@ -43,9 +43,12 @@ EXPERIMENT: FORMFACTOR: - 10.1021/jp511159q/1 bioschema_properties: - name: Molecular dynamics trajectory of a POPE bilayer at 308 K (Charmm-Drude polarizable2023, OPENMM, 200 ns) [NMRlipids simulation 751] + name: Molecular dynamics trajectory of a POPE bilayer at 308 K (Charmm-Drude polarizable2023, + OPENMM, 200 ns) [NMRlipids simulation 751] alternateName: POPE_CHARMMdrude2023_308K - description: Molecular dynamics trajectory of a lipid bilayer of 72 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) at 308 K. Simulated with Charmm-Drude polarizable2023 in OPENMM for 200 ns (24624 atoms). Deposited as NMRlipids Databank simulation 751 and available from https://doi.org/10.5281/zenodo.7916494. + description: Molecular dynamics trajectory of a lipid bilayer of 72 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) + at 308 K. Simulated with Charmm-Drude polarizable2023 in OPENMM for 200 ns (24624 + atoms). Deposited as NMRlipids Databank simulation 751 and available from https://doi.org/10.5281/zenodo.7916494. sameAs: https://doi.org/10.5281/zenodo.7916494 datePublished: '2023-05-09' license: @@ -135,7 +138,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.7916494 identifier: 10.5281/zenodo.7916494 url: https://doi.org/10.5281/zenodo.7916494 - name: OpenMM simulations of POPE using the CHARMM Drude2023 force field in xtc format + name: OpenMM simulations of POPE using the CHARMM Drude2023 force field in xtc + format publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/7f5/f1d/7f5f1d8eba326b558ca7fe378643d64fe4bace31/73f533dcf83fcc06f19cd6d755408269b36853d8/README.yaml b/Simulations/7f5/f1d/7f5f1d8eba326b558ca7fe378643d64fe4bace31/73f533dcf83fcc06f19cd6d755408269b36853d8/README.yaml index 4079d0e9e5..48b1ae02a4 100644 --- a/Simulations/7f5/f1d/7f5f1d8eba326b558ca7fe378643d64fe4bace31/73f533dcf83fcc06f19cd6d755408269b36853d8/README.yaml +++ b/Simulations/7f5/f1d/7f5f1d8eba326b558ca7fe378643d64fe4bace31/73f533dcf83fcc06f19cd6d755408269b36853d8/README.yaml @@ -55,9 +55,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 145 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPS/POT (71:14:14) bilayer at 298 K (ECC-lipids, SPC water model, ECC-ions, GROMACS 2018.0, 984 ns) [NMRlipids simulation 145] + name: Molecular dynamics trajectory of a POPC/POPS/POT (71:14:14) bilayer at 298 + K (ECC-lipids, SPC water model, ECC-ions, GROMACS 2018.0, 984 ns) [NMRlipids simulation + 145] alternateName: 12POPS_60POPC_3600SOL_12POT_298K_ECC-lipid - description: Molecular dynamics trajectory of a lipid bilayer of 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 71 mol%), 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 14 mol%) and 12 POT (14 mol%) at 298 K. Simulated with ECC-lipids, SPC water model, ECC-ions in GROMACS 2018.0 for 984 ns (20376 atoms). Deposited as NMRlipids Databank simulation 145 and available from https://doi.org/10.5281/zenodo.1488094. + description: Molecular dynamics trajectory of a lipid bilayer of 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 71 mol%), 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 14 mol%) + and 12 POT (14 mol%) at 298 K. Simulated with ECC-lipids, SPC water model, ECC-ions + in GROMACS 2018.0 for 984 ns (20376 atoms). Deposited as NMRlipids Databank simulation + 145 and available from https://doi.org/10.5281/zenodo.1488094. sameAs: https://doi.org/10.5281/zenodo.1488094 datePublished: '2018-11-14' license: @@ -148,7 +154,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1488094 identifier: 10.5281/zenodo.1488094 url: https://doi.org/10.5281/zenodo.1488094 - name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS (various mixtures) with ECC-lipids force field, and Na+ (K+) counterions + name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS + (various mixtures) with ECC-lipids force field, and Na+ (K+) counterions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/7f6/051/7f60515152693b6ca40d762b89019635b93f3ece/55e587074b9ccd85713f574f4c0aa85f4c78dd09/README.yaml b/Simulations/7f6/051/7f60515152693b6ca40d762b89019635b93f3ece/55e587074b9ccd85713f574f4c0aa85f4c78dd09/README.yaml index ad12c40bc6..c6d1a18815 100644 --- a/Simulations/7f6/051/7f60515152693b6ca40d762b89019635b93f3ece/55e587074b9ccd85713f574f4c0aa85f4c78dd09/README.yaml +++ b/Simulations/7f6/051/7f60515152693b6ca40d762b89019635b93f3ece/55e587074b9ccd85713f574f4c0aa85f4c78dd09/README.yaml @@ -49,9 +49,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 659 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (71:29) bilayer at 298.15 K (Slipids, GROMACS 2021, 1001 ns) [NMRlipids simulation 659] + name: Molecular dynamics trajectory of a POPC/CHOL (71:29) bilayer at 298.15 K (Slipids, + GROMACS 2021, 1001 ns) [NMRlipids simulation 659] alternateName: Slipids_POPC_CHOL29_M - description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 71 mol%) and 104 CHOL (cholesterol, 29 mol%) at 298.15 K. Simulated with Slipids in GROMACS 2021 for 1001 ns (96000 atoms). Deposited as NMRlipids Databank simulation 659 and available from https://doi.org/10.5281/zenodo.7022749. + description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 71 mol%) and 104 CHOL (cholesterol, 29 mol%) at 298.15 K. Simulated with Slipids + in GROMACS 2021 for 1001 ns (96000 atoms). Deposited as NMRlipids Databank simulation + 659 and available from https://doi.org/10.5281/zenodo.7022749. sameAs: https://doi.org/10.5281/zenodo.7022749 datePublished: '2022-08-23' license: diff --git a/Simulations/7f6/73c/7f673c119523044d7e2d5986e8db7ab5c5a18e64/545850139a3d54a3d727c323db0355e40bb6d032/README.yaml b/Simulations/7f6/73c/7f673c119523044d7e2d5986e8db7ab5c5a18e64/545850139a3d54a3d727c323db0355e40bb6d032/README.yaml index ef58d39161..a7b6778ebe 100644 --- a/Simulations/7f6/73c/7f673c119523044d7e2d5986e8db7ab5c5a18e64/545850139a3d54a3d727c323db0355e40bb6d032/README.yaml +++ b/Simulations/7f6/73c/7f673c119523044d7e2d5986e8db7ab5c5a18e64/545850139a3d54a3d727c323db0355e40bb6d032/README.yaml @@ -50,9 +50,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/3 ID: 660 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (89:11) bilayer at 298.15 K (MacRog, GROMACS 2021, 1001 ns) [NMRlipids simulation 660] + name: Molecular dynamics trajectory of a POPC/CHOL (89:11) bilayer at 298.15 K (MacRog, + GROMACS 2021, 1001 ns) [NMRlipids simulation 660] alternateName: MacRog_POPC_CHOL11_L - description: Molecular dynamics trajectory of a lipid bilayer of 1024 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 89 mol%) and 128 CHOL (cholesterol, 11 mol%) at 298.15 K. Simulated with MacRog in GROMACS 2021 for 1001 ns (319488 atoms). Deposited as NMRlipids Databank simulation 660 and available from https://doi.org/10.5281/zenodo.7061800. + description: Molecular dynamics trajectory of a lipid bilayer of 1024 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 89 mol%) and 128 CHOL (cholesterol, 11 mol%) at 298.15 K. Simulated with MacRog + in GROMACS 2021 for 1001 ns (319488 atoms). Deposited as NMRlipids Databank simulation + 660 and available from https://doi.org/10.5281/zenodo.7061800. sameAs: https://doi.org/10.5281/zenodo.7061800 datePublished: '2022-09-08' license: diff --git a/Simulations/7f6/fbc/7f6fbc9ec469b1d33d2ec93cccdd86768443988f/f7a6d748844cb56fec39dd0c2f27b9483a291114/README.yaml b/Simulations/7f6/fbc/7f6fbc9ec469b1d33d2ec93cccdd86768443988f/f7a6d748844cb56fec39dd0c2f27b9483a291114/README.yaml index d7bde7be50..5a2a097dd4 100644 --- a/Simulations/7f6/fbc/7f6fbc9ec469b1d33d2ec93cccdd86768443988f/f7a6d748844cb56fec39dd0c2f27b9483a291114/README.yaml +++ b/Simulations/7f6/fbc/7f6fbc9ec469b1d33d2ec93cccdd86768443988f/f7a6d748844cb56fec39dd0c2f27b9483a291114/README.yaml @@ -51,9 +51,13 @@ WARNINGS: PBC: z-jumps ID: 31 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (58:21:21) bilayer at 303 K (CHARMM36, GROMACS 4.5, 40 ns) [NMRlipids simulation 31] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (58:21:21) bilayer at 303 + K (CHARMM36, GROMACS 4.5, 40 ns) [NMRlipids simulation 31] alternateName: 72POPC_2190SOL_26CLA_26NA_303K - description: Molecular dynamics trajectory of a lipid bilayer of 72 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 58 mol%), 26 CLA (21 mol%) and 26 SOD (21 mol%) at 303 K. Simulated with CHARMM36 in GROMACS 4.5 for 40 ns (16270 atoms). Deposited as NMRlipids Databank simulation 31 and available from https://doi.org/10.5281/zenodo.32497. + description: Molecular dynamics trajectory of a lipid bilayer of 72 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 58 mol%), 26 CLA (21 mol%) and 26 SOD (21 mol%) at 303 K. Simulated with CHARMM36 + in GROMACS 4.5 for 40 ns (16270 atoms). Deposited as NMRlipids Databank simulation + 31 and available from https://doi.org/10.5281/zenodo.32497. sameAs: https://doi.org/10.5281/zenodo.32497 datePublished: '2015-10-21' license: @@ -141,7 +145,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.32497 identifier: 10.5281/zenodo.32497 url: https://doi.org/10.5281/zenodo.32497 - name: Md Simulation Trajectory And Related Files For Popc Bilayer With 690Mm Nacl (Charmm36, Gromacs 4.5) + name: Md Simulation Trajectory And Related Files For Popc Bilayer With 690Mm Nacl + (Charmm36, Gromacs 4.5) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/7fb/54a/7fb54abf48f15110055b7a49103d78b99c3a4b0c/5623db5d939c5614eab52dd575ebe96182a3b15a/README.yaml b/Simulations/7fb/54a/7fb54abf48f15110055b7a49103d78b99c3a4b0c/5623db5d939c5614eab52dd575ebe96182a3b15a/README.yaml index f6200796a4..e9d9172f03 100644 --- a/Simulations/7fb/54a/7fb54abf48f15110055b7a49103d78b99c3a4b0c/5623db5d939c5614eab52dd575ebe96182a3b15a/README.yaml +++ b/Simulations/7fb/54a/7fb54abf48f15110055b7a49103d78b99c3a4b0c/5623db5d939c5614eab52dd575ebe96182a3b15a/README.yaml @@ -44,9 +44,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 173 bioschema_properties: - name: Molecular dynamics trajectory of a POPE bilayer at 303 K (Berger, GROMACS 4.0.7, 100 ns) [NMRlipids simulation 173] + name: Molecular dynamics trajectory of a POPE bilayer at 303 K (Berger, GROMACS + 4.0.7, 100 ns) [NMRlipids simulation 173] alternateName: 128POPE_3552SOL_303K_Berger_v2 - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) at 303 K. Simulated with Berger in GROMACS 4.0.7 for 100 ns (17312 atoms). Deposited as NMRlipids Databank simulation 173 and available from https://doi.org/10.5281/zenodo.1293891. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) + at 303 K. Simulated with Berger in GROMACS 4.0.7 for 100 ns (17312 atoms). Deposited + as NMRlipids Databank simulation 173 and available from https://doi.org/10.5281/zenodo.1293891. sameAs: https://doi.org/10.5281/zenodo.1293891 datePublished: '2018-06-20' license: diff --git a/Simulations/7ff/03d/7ff03d6c44fe48f95b15bb4563a17b8cb9249745/954d3cd3142844a0e3c6b5ca176a6e300f45effd/README.yaml b/Simulations/7ff/03d/7ff03d6c44fe48f95b15bb4563a17b8cb9249745/954d3cd3142844a0e3c6b5ca176a6e300f45effd/README.yaml index 3cdb8c19c8..b2642ffc8d 100644 --- a/Simulations/7ff/03d/7ff03d6c44fe48f95b15bb4563a17b8cb9249745/954d3cd3142844a0e3c6b5ca176a6e300f45effd/README.yaml +++ b/Simulations/7ff/03d/7ff03d6c44fe48f95b15bb4563a17b8cb9249745/954d3cd3142844a0e3c6b5ca176a6e300f45effd/README.yaml @@ -43,9 +43,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 816 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 300 K (OPLS3e, GROMACS 2019-4, 495 ns) [NMRlipids simulation 816] + name: Molecular dynamics trajectory of a POPC bilayer at 300 K (OPLS3e, GROMACS + 2019-4, 495 ns) [NMRlipids simulation 816] alternateName: 200POPC_2kSOL_300K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 300 K. Simulated with OPLS3e in GROMACS 2019-4 for 495 ns (32800 atoms). Deposited as NMRlipids Databank simulation 816 and available from https://doi.org/10.5281/zenodo.10183926. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 300 K. Simulated with OPLS3e in GROMACS 2019-4 for 495 ns (32800 atoms). Deposited + as NMRlipids Databank simulation 816 and available from https://doi.org/10.5281/zenodo.10183926. sameAs: https://doi.org/10.5281/zenodo.10183926 datePublished: '2022' license: diff --git a/Simulations/803/9d5/8039d537f1f2143d20248b72c9b87d81dbb4cd41/8039d537f1f2143d20248b72c9b87d81dbb4cd41/README.yaml b/Simulations/803/9d5/8039d537f1f2143d20248b72c9b87d81dbb4cd41/8039d537f1f2143d20248b72c9b87d81dbb4cd41/README.yaml index fb57448217..0d94ac5f83 100644 --- a/Simulations/803/9d5/8039d537f1f2143d20248b72c9b87d81dbb4cd41/8039d537f1f2143d20248b72c9b87d81dbb4cd41/README.yaml +++ b/Simulations/803/9d5/8039d537f1f2143d20248b72c9b87d81dbb4cd41/8039d537f1f2143d20248b72c9b87d81dbb4cd41/README.yaml @@ -46,9 +46,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 741 bioschema_properties: - name: Molecular dynamics trajectory of a DOPC/CLA/CAL (60:27:13) bilayer at 303 K (AMOEBA, OPENMM v7.5.1, 218 ns) [NMRlipids simulation 741] + name: Molecular dynamics trajectory of a DOPC/CLA/CAL (60:27:13) bilayer at 303 + K (AMOEBA, OPENMM v7.5.1, 218 ns) [NMRlipids simulation 741] alternateName: DOPC_450mM_CaCl2_at_303K_with_AMOEBA - description: Molecular dynamics trajectory of a lipid bilayer of 72 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, 60 mol%), 32 CLA (27 mol%) and 16 CAL (13 mol%) at 303 K. Simulated with AMOEBA in OPENMM v7.5.1 for 218 ns (18624 atoms). Deposited as NMRlipids Databank simulation 741 and available from https://doi.org/10.5281/zenodo.7604842. + description: Molecular dynamics trajectory of a lipid bilayer of 72 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, + 60 mol%), 32 CLA (27 mol%) and 16 CAL (13 mol%) at 303 K. Simulated with AMOEBA + in OPENMM v7.5.1 for 218 ns (18624 atoms). Deposited as NMRlipids Databank simulation + 741 and available from https://doi.org/10.5281/zenodo.7604842. sameAs: https://doi.org/10.5281/zenodo.7604842 datePublished: '2022-12-11' license: @@ -136,7 +140,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.7604842 identifier: 10.5281/zenodo.7604842 url: https://doi.org/10.5281/zenodo.7604842 - name: MD Simulation data for a pure DOPC bilayer (450 mM CaCl2) with AMOEBA force field + OpenMM + name: MD Simulation data for a pure DOPC bilayer (450 mM CaCl2) with AMOEBA force + field + OpenMM publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/808/c7a/808c7aeb6d972c46e68b73262779414b4dad7295/5f945ed9d7f9e2cd38133fec4afb757eb7db3542/README.yaml b/Simulations/808/c7a/808c7aeb6d972c46e68b73262779414b4dad7295/5f945ed9d7f9e2cd38133fec4afb757eb7db3542/README.yaml index 5c07694c06..7b30278947 100644 --- a/Simulations/808/c7a/808c7aeb6d972c46e68b73262779414b4dad7295/5f945ed9d7f9e2cd38133fec4afb757eb7db3542/README.yaml +++ b/Simulations/808/c7a/808c7aeb6d972c46e68b73262779414b4dad7295/5f945ed9d7f9e2cd38133fec4afb757eb7db3542/README.yaml @@ -51,9 +51,13 @@ WARNINGS: PBC: z-jumps ID: 372 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (49:25:25) bilayer at 303 K (CHARMM36, GROMACS 4.5, 60 ns) [NMRlipids simulation 372] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (49:25:25) bilayer at 303 + K (CHARMM36, GROMACS 4.5, 60 ns) [NMRlipids simulation 372] alternateName: 72POPC_2168SOL_37CLA_37NA_303K - description: Molecular dynamics trajectory of a lipid bilayer of 72 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 49 mol%), 37 CLA (25 mol%) and 37 SOD (25 mol%) at 303 K. Simulated with CHARMM36 in GROMACS 4.5 for 60 ns (16226 atoms). Deposited as NMRlipids Databank simulation 372 and available from https://doi.org/10.5281/zenodo.32498. + description: Molecular dynamics trajectory of a lipid bilayer of 72 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 49 mol%), 37 CLA (25 mol%) and 37 SOD (25 mol%) at 303 K. Simulated with CHARMM36 + in GROMACS 4.5 for 60 ns (16226 atoms). Deposited as NMRlipids Databank simulation + 372 and available from https://doi.org/10.5281/zenodo.32498. sameAs: https://doi.org/10.5281/zenodo.32498 datePublished: '2015-10-21' license: @@ -141,7 +145,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.32498 identifier: 10.5281/zenodo.32498 url: https://doi.org/10.5281/zenodo.32498 - name: Md Simulation Trajectory And Related Files For Popc Bilayer With 950Mm Nacl (Charmm36, Gromacs 4.5) + name: Md Simulation Trajectory And Related Files For Popc Bilayer With 950Mm Nacl + (Charmm36, Gromacs 4.5) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/80e/71c/80e71c6616d7eb421861bf4edce710e1fc960984/582a7ab9fa1f0aa9de70eb9d36bc47a52db720b0/README.yaml b/Simulations/80e/71c/80e71c6616d7eb421861bf4edce710e1fc960984/582a7ab9fa1f0aa9de70eb9d36bc47a52db720b0/README.yaml index 75e15cadfe..2dfe01c2b7 100644 --- a/Simulations/80e/71c/80e71c6616d7eb421861bf4edce710e1fc960984/582a7ab9fa1f0aa9de70eb9d36bc47a52db720b0/README.yaml +++ b/Simulations/80e/71c/80e71c6616d7eb421861bf4edce710e1fc960984/582a7ab9fa1f0aa9de70eb9d36bc47a52db720b0/README.yaml @@ -52,9 +52,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 556 bioschema_properties: - name: Molecular dynamics trajectory of a POPG/SOD/POPE (43:43:14) bilayer at 310 K (Lipid17, GROMACS 2018.3, 100 ns) [NMRlipids simulation 556] + name: Molecular dynamics trajectory of a POPG/SOD/POPE (43:43:14) bilayer at 310 + K (Lipid17, GROMACS 2018.3, 100 ns) [NMRlipids simulation 556] alternateName: POPG_POPE_25000SOL_374SOD_310K - description: Molecular dynamics trajectory of a lipid bilayer of 374 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 43 mol%), 374 SOD (43 mol%) and 126 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 14 mol%) at 310 K. Simulated with Lipid17 in GROMACS 2018.3 for 100 ns (138622 atoms). Deposited as NMRlipids Databank simulation 556 and available from https://doi.org/10.5281/zenodo.3256490. + description: Molecular dynamics trajectory of a lipid bilayer of 374 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, + 43 mol%), 374 SOD (43 mol%) and 126 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, + 14 mol%) at 310 K. Simulated with Lipid17 in GROMACS 2018.3 for 100 ns (138622 + atoms). Deposited as NMRlipids Databank simulation 556 and available from https://doi.org/10.5281/zenodo.3256490. sameAs: https://doi.org/10.5281/zenodo.3256490 datePublished: '2019-06-25' license: diff --git a/Simulations/813/2bc/8132bc41c60e0156caeb7a99f11efb3206fa1619/69de81ab0e12664c93685826a4b1734bcde763fe/README.yaml b/Simulations/813/2bc/8132bc41c60e0156caeb7a99f11efb3206fa1619/69de81ab0e12664c93685826a4b1734bcde763fe/README.yaml index 4a611c8427..0b5ae56fb8 100644 --- a/Simulations/813/2bc/8132bc41c60e0156caeb7a99f11efb3206fa1619/69de81ab0e12664c93685826a4b1734bcde763fe/README.yaml +++ b/Simulations/813/2bc/8132bc41c60e0156caeb7a99f11efb3206fa1619/69de81ab0e12664c93685826a4b1734bcde763fe/README.yaml @@ -44,9 +44,12 @@ EXPERIMENT: PYPC: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a PYPC bilayer at 333.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 627] + name: Molecular dynamics trajectory of a PYPC bilayer at 333.15 K (CHARMM36, GROMACS, + 1001 ns) [NMRlipids simulation 627] alternateName: 256PYPC_12800SOL_333K - description: Molecular dynamics trajectory of a lipid bilayer of 256 PYPC (1-(16:0)-2-(16:1$^\Delta9$)-sn-glycero-3-phosphocholine) at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (71168 atoms). Deposited as NMRlipids Databank simulation 627 and available from https://doi.org/10.5281/zenodo.6943413. + description: Molecular dynamics trajectory of a lipid bilayer of 256 PYPC (1-(16:0)-2-(16:1$^\Delta9$)-sn-glycero-3-phosphocholine) + at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (71168 atoms). Deposited + as NMRlipids Databank simulation 627 and available from https://doi.org/10.5281/zenodo.6943413. sameAs: https://doi.org/10.5281/zenodo.6943413 datePublished: '2022-07-30' license: @@ -134,7 +137,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.6943413 identifier: 10.5281/zenodo.6943413 url: https://doi.org/10.5281/zenodo.6943413 - name: Simulations of different single-component bilayers, three different system sizes + name: Simulations of different single-component bilayers, three different system + sizes publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/814/7cf/8147cf489ede30f8e44247cb5f5b2b3a72649d88/1cb6538530c40abb28ad1480cb53f8faca939de8/README.yaml b/Simulations/814/7cf/8147cf489ede30f8e44247cb5f5b2b3a72649d88/1cb6538530c40abb28ad1480cb53f8faca939de8/README.yaml index 56d5f9dfd7..303b2c5146 100644 --- a/Simulations/814/7cf/8147cf489ede30f8e44247cb5f5b2b3a72649d88/1cb6538530c40abb28ad1480cb53f8faca939de8/README.yaml +++ b/Simulations/814/7cf/8147cf489ede30f8e44247cb5f5b2b3a72649d88/1cb6538530c40abb28ad1480cb53f8faca939de8/README.yaml @@ -50,9 +50,13 @@ WARNINGS: PBC: z-jumps ID: 85 bioschema_properties: - name: Molecular dynamics trajectory of a CHOL/POPC (50:50) bilayer at 303 K (Lipid14, GROMACS 5.0.4, 200 ns) [NMRlipids simulation 85] + name: Molecular dynamics trajectory of a CHOL/POPC (50:50) bilayer at 303 K (Lipid14, + GROMACS 5.0.4, 200 ns) [NMRlipids simulation 85] alternateName: 64POPC_64CHOL_3968SOL_303K - description: Molecular dynamics trajectory of a lipid bilayer of 64 CHOL (cholesterol, 50 mol%) and 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 50 mol%) at 303 K. Simulated with Lipid14 in GROMACS 5.0.4 for 200 ns (25216 atoms). Deposited as NMRlipids Databank simulation 85 and available from https://doi.org/10.5281/zenodo.3871006. + description: Molecular dynamics trajectory of a lipid bilayer of 64 CHOL (cholesterol, + 50 mol%) and 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 50 mol%) + at 303 K. Simulated with Lipid14 in GROMACS 5.0.4 for 200 ns (25216 atoms). Deposited + as NMRlipids Databank simulation 85 and available from https://doi.org/10.5281/zenodo.3871006. sameAs: https://doi.org/10.5281/zenodo.3871006 datePublished: '2020-06-01' license: @@ -141,7 +145,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3871006 identifier: 10.5281/zenodo.3871006 url: https://doi.org/10.5281/zenodo.3871006 - name: 'MD simulations of bilayers containing POPC and Cholesterol: 64POPC_64CHL_31Nwat_neutral (lipid14)' + name: 'MD simulations of bilayers containing POPC and Cholesterol: 64POPC_64CHL_31Nwat_neutral + (lipid14)' publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/815/ad3/815ad324c34bfdfcbdc34ead95481bf38723c42b/657393f95833364bff072b6824252dbd998c31c9/README.yaml b/Simulations/815/ad3/815ad324c34bfdfcbdc34ead95481bf38723c42b/657393f95833364bff072b6824252dbd998c31c9/README.yaml index 2fc2577fda..5117bf1230 100644 --- a/Simulations/815/ad3/815ad324c34bfdfcbdc34ead95481bf38723c42b/657393f95833364bff072b6824252dbd998c31c9/README.yaml +++ b/Simulations/815/ad3/815ad324c34bfdfcbdc34ead95481bf38723c42b/657393f95833364bff072b6824252dbd998c31c9/README.yaml @@ -49,9 +49,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 373 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (60:40) bilayer at 310 K (Slipids, GROMACS 4.6, 500 ns) [NMRlipids simulation 373] + name: Molecular dynamics trajectory of a POPC/CHOL (60:40) bilayer at 310 K (Slipids, + GROMACS 4.6, 500 ns) [NMRlipids simulation 373] alternateName: 200POPC_9000SOL_134CHOL_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 60 mol%) and 134 CHOL (cholesterol, 40 mol%) at 310 K. Simulated with Slipids in GROMACS 4.6 for 500 ns (81806 atoms). Deposited as NMRlipids Databank simulation 373 and available from https://doi.org/10.5281/zenodo.3243329. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 60 mol%) and 134 CHOL (cholesterol, 40 mol%) at 310 K. Simulated with Slipids + in GROMACS 4.6 for 500 ns (81806 atoms). Deposited as NMRlipids Databank simulation + 373 and available from https://doi.org/10.5281/zenodo.3243329. sameAs: https://doi.org/10.5281/zenodo.3243329 datePublished: '2016-09-18' license: diff --git a/Simulations/818/441/818441b1a180862d99b4c2980f988a0e67e6fbb4/edd860b5790aafabeffc15055efdbdada696a1a3/README.yaml b/Simulations/818/441/818441b1a180862d99b4c2980f988a0e67e6fbb4/edd860b5790aafabeffc15055efdbdada696a1a3/README.yaml index fc54314ef2..390b8e4c1c 100644 --- a/Simulations/818/441/818441b1a180862d99b4c2980f988a0e67e6fbb4/edd860b5790aafabeffc15055efdbdada696a1a3/README.yaml +++ b/Simulations/818/441/818441b1a180862d99b4c2980f988a0e67e6fbb4/edd860b5790aafabeffc15055efdbdada696a1a3/README.yaml @@ -55,9 +55,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 231 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (48:35:17) bilayer at 310.15 K (CHARMM36 NBFIX Kim, GROMACS, 361 ns) [NMRlipids simulation 231] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (48:35:17) bilayer at 310.15 + K (CHARMM36 NBFIX Kim, GROMACS, 361 ns) [NMRlipids simulation 231] alternateName: 200POPC_9000SOL_73CAL_146CLA_310K_NBFIXKim - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 48 mol%), 146 CLA (35 mol%) and 73 CAL (17 mol%) at 310.15 K. Simulated with CHARMM36 NBFIX Kim in GROMACS for 361 ns (54019 atoms). Deposited as NMRlipids Databank simulation 231 and available from https://doi.org/10.5281/zenodo.3434396. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 48 mol%), 146 CLA (35 mol%) and 73 CAL (17 mol%) at 310.15 K. Simulated with CHARMM36 + NBFIX Kim in GROMACS for 361 ns (54019 atoms). Deposited as NMRlipids Databank + simulation 231 and available from https://doi.org/10.5281/zenodo.3434396. sameAs: https://doi.org/10.5281/zenodo.3434396 datePublished: '2019-09-17' license: diff --git a/Simulations/81c/ec4/81cec484d668f6dae7a11c018313390200e0c0c0/0f3a4fe20d976d359093fbf2bb228cbfa4190800/README.yaml b/Simulations/81c/ec4/81cec484d668f6dae7a11c018313390200e0c0c0/0f3a4fe20d976d359093fbf2bb228cbfa4190800/README.yaml index 3f71100285..5f54f74296 100644 --- a/Simulations/81c/ec4/81cec484d668f6dae7a11c018313390200e0c0c0/0f3a4fe20d976d359093fbf2bb228cbfa4190800/README.yaml +++ b/Simulations/81c/ec4/81cec484d668f6dae7a11c018313390200e0c0c0/0f3a4fe20d976d359093fbf2bb228cbfa4190800/README.yaml @@ -50,9 +50,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 875 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (76:12:12) bilayer at 300 K (CHARMM36, GROMACS 2019.5, 455 ns) [NMRlipids simulation 875] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (76:12:12) bilayer at 300 + K (CHARMM36, GROMACS 2019.5, 455 ns) [NMRlipids simulation 875] alternateName: POPC, 44 w/l, 300 K, 0.2 M NaCl - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 76 mol%), 32 CLA (12 mol%) and 32 SOD (12 mol%) at 300 K. Simulated with CHARMM36 in GROMACS 2019.5 for 455 ns (53504 atoms). Deposited as NMRlipids Databank simulation 875 and available from https://doi.org/10.5281/zenodo.6342175. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 76 mol%), 32 CLA (12 mol%) and 32 SOD (12 mol%) at 300 K. Simulated with CHARMM36 + in GROMACS 2019.5 for 455 ns (53504 atoms). Deposited as NMRlipids Databank simulation + 875 and available from https://doi.org/10.5281/zenodo.6342175. sameAs: https://doi.org/10.5281/zenodo.6342175 datePublished: '2022-03-09' license: diff --git a/Simulations/81e/7ec/81e7ec74dd701b371a2143df85c13c4cb83a0aab/f10c789c6abcb409cbfea745732399ac301d8828/README.yaml b/Simulations/81e/7ec/81e7ec74dd701b371a2143df85c13c4cb83a0aab/f10c789c6abcb409cbfea745732399ac301d8828/README.yaml index 61b05fb190..ee54b4da33 100644 --- a/Simulations/81e/7ec/81e7ec74dd701b371a2143df85c13c4cb83a0aab/f10c789c6abcb409cbfea745732399ac301d8828/README.yaml +++ b/Simulations/81e/7ec/81e7ec74dd701b371a2143df85c13c4cb83a0aab/f10c789c6abcb409cbfea745732399ac301d8828/README.yaml @@ -49,9 +49,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 453 bioschema_properties: - name: Molecular dynamics trajectory of a POPE/SDG (91:9) bilayer at 310 K (Lipid17, GROMACS 18.6, 2100 ns) [NMRlipids simulation 453] + name: Molecular dynamics trajectory of a POPE/SDG (91:9) bilayer at 310 K (Lipid17, + GROMACS 18.6, 2100 ns) [NMRlipids simulation 453] alternateName: 9.4%SDGinPOPEwithLipid17 - description: Molecular dynamics trajectory of a lipid bilayer of 116 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 91 mol%) and 12 SDG (1-stearoyl-2-docosahexaenoyl-sn-glycerol, 9 mol%) at 310 K. Simulated with Lipid17 in GROMACS 18.6 for 2100 ns (35140 atoms). Deposited as NMRlipids Databank simulation 453 and available from https://doi.org/10.5281/zenodo.6778139. + description: Molecular dynamics trajectory of a lipid bilayer of 116 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, + 91 mol%) and 12 SDG (1-stearoyl-2-docosahexaenoyl-sn-glycerol, 9 mol%) at 310 + K. Simulated with Lipid17 in GROMACS 18.6 for 2100 ns (35140 atoms). Deposited + as NMRlipids Databank simulation 453 and available from https://doi.org/10.5281/zenodo.6778139. sameAs: https://doi.org/10.5281/zenodo.6778139 datePublished: '2022-06-29' license: diff --git a/Simulations/821/08d/82108df2eeae8ee1ff2a9dfb390b730edd3e9a26/0476e26b6c2c5d789d51c0c7e5cf646a1608a433/README.yaml b/Simulations/821/08d/82108df2eeae8ee1ff2a9dfb390b730edd3e9a26/0476e26b6c2c5d789d51c0c7e5cf646a1608a433/README.yaml index 1e3c209e89..3d84ceb46e 100644 --- a/Simulations/821/08d/82108df2eeae8ee1ff2a9dfb390b730edd3e9a26/0476e26b6c2c5d789d51c0c7e5cf646a1608a433/README.yaml +++ b/Simulations/821/08d/82108df2eeae8ee1ff2a9dfb390b730edd3e9a26/0476e26b6c2c5d789d51c0c7e5cf646a1608a433/README.yaml @@ -48,9 +48,12 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/1 ID: 43 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 300 K (ECC-lipids, GROMACS 5.1.4, 300 ns) [NMRlipids simulation 43] + name: Molecular dynamics trajectory of a POPC bilayer at 300 K (ECC-lipids, GROMACS + 5.1.4, 300 ns) [NMRlipids simulation 43] alternateName: 128POPC_6400SOL_300K_OPC3model - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 300 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 300 ns (36352 atoms). Deposited as NMRlipids Databank simulation 43 and available from https://doi.org/10.5281/zenodo.1118980. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 300 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 300 ns (36352 atoms). + Deposited as NMRlipids Databank simulation 43 and available from https://doi.org/10.5281/zenodo.1118980. sameAs: https://doi.org/10.5281/zenodo.1118980 datePublished: '2017-12-19' license: @@ -142,7 +145,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1118980 identifier: 10.5281/zenodo.1118980 url: https://doi.org/10.5281/zenodo.1118980 - name: Simulations Of Popc Lipid Bilayer In Water Solution At Various Nacl And Cacl2 Concentrations Using Ecc-Popc Force Field And Various Water Models + name: Simulations Of Popc Lipid Bilayer In Water Solution At Various Nacl And + Cacl2 Concentrations Using Ecc-Popc Force Field And Various Water Models publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/821/0ab/8210abcb2e2d5c8a91f0a880896559e054b72a5e/66215f706d70b179a461998cbc065beef1992c8d/README.yaml b/Simulations/821/0ab/8210abcb2e2d5c8a91f0a880896559e054b72a5e/66215f706d70b179a461998cbc065beef1992c8d/README.yaml index 39b1d20a66..4fe60aab3a 100644 --- a/Simulations/821/0ab/8210abcb2e2d5c8a91f0a880896559e054b72a5e/66215f706d70b179a461998cbc065beef1992c8d/README.yaml +++ b/Simulations/821/0ab/8210abcb2e2d5c8a91f0a880896559e054b72a5e/66215f706d70b179a461998cbc065beef1992c8d/README.yaml @@ -50,9 +50,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 873 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (38:31:31) bilayer at 300 K (CHARMM36, GROMACS 2019.5, 485 ns) [NMRlipids simulation 873] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (38:31:31) bilayer at 300 + K (CHARMM36, GROMACS 2019.5, 485 ns) [NMRlipids simulation 873] alternateName: POPC, 44 w/l, 300 K, 1 M NaCl - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 38 mol%), 160 CLA (31 mol%) and 160 SOD (31 mol%) at 300 K. Simulated with CHARMM36 in GROMACS 2019.5 for 485 ns (53760 atoms). Deposited as NMRlipids Databank simulation 873 and available from https://doi.org/10.5281/zenodo.6342652. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 38 mol%), 160 CLA (31 mol%) and 160 SOD (31 mol%) at 300 K. Simulated with CHARMM36 + in GROMACS 2019.5 for 485 ns (53760 atoms). Deposited as NMRlipids Databank simulation + 873 and available from https://doi.org/10.5281/zenodo.6342652. sameAs: https://doi.org/10.5281/zenodo.6342652 datePublished: '2022-03-10' license: diff --git a/Simulations/82e/424/82e42412f1383f19441f90baf20721ab773ce1fa/45b6ab86e2a313b1be49ac29d8edb6b3688a0421/README.yaml b/Simulations/82e/424/82e42412f1383f19441f90baf20721ab773ce1fa/45b6ab86e2a313b1be49ac29d8edb6b3688a0421/README.yaml index 1ededee4b9..25b9d68a9a 100644 --- a/Simulations/82e/424/82e42412f1383f19441f90baf20721ab773ce1fa/45b6ab86e2a313b1be49ac29d8edb6b3688a0421/README.yaml +++ b/Simulations/82e/424/82e42412f1383f19441f90baf20721ab773ce1fa/45b6ab86e2a313b1be49ac29d8edb6b3688a0421/README.yaml @@ -51,9 +51,13 @@ EXPERIMENT: GB3: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD/GB3 (75:11:11:4) bilayer at 310 K (CHARMM36m, GROMACS 2019.4/2020, 7255 ns) [NMRlipids simulation 850] + name: Molecular dynamics trajectory of a POPC/CLA/SOD/GB3 (75:11:11:4) bilayer at + 310 K (CHARMM36m, GROMACS 2019.4/2020, 7255 ns) [NMRlipids simulation 850] alternateName: POPC:Gb3_run1(95:5 mol:mol) - description: Molecular dynamics trajectory of a lipid bilayer of 190 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 75 mol%), 27 CLA (11 mol%), 27 SOD (11 mol%) and 10 GB3 (Gb3(d18:1/24:0), 4 mol%) at 310 K. Simulated with CHARMM36m in GROMACS 2019.4/2020 for 7255 ns (74381 atoms). Deposited as NMRlipids Databank simulation 850 and available from https://doi.org/10.5281/zenodo.10635871. + description: Molecular dynamics trajectory of a lipid bilayer of 190 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 75 mol%), 27 CLA (11 mol%), 27 SOD (11 mol%) and 10 GB3 (Gb3(d18:1/24:0), 4 mol%) + at 310 K. Simulated with CHARMM36m in GROMACS 2019.4/2020 for 7255 ns (74381 atoms). + Deposited as NMRlipids Databank simulation 850 and available from https://doi.org/10.5281/zenodo.10635871. sameAs: https://doi.org/10.5281/zenodo.10635871 datePublished: '2024-02-08' license: diff --git a/Simulations/82e/424/82e42412f1383f19441f90baf20721ab773ce1fa/6fd7d3a864973fb14dee318fc08f64f33a33e661/README.yaml b/Simulations/82e/424/82e42412f1383f19441f90baf20721ab773ce1fa/6fd7d3a864973fb14dee318fc08f64f33a33e661/README.yaml index 55853f3149..ed9c46182a 100644 --- a/Simulations/82e/424/82e42412f1383f19441f90baf20721ab773ce1fa/6fd7d3a864973fb14dee318fc08f64f33a33e661/README.yaml +++ b/Simulations/82e/424/82e42412f1383f19441f90baf20721ab773ce1fa/6fd7d3a864973fb14dee318fc08f64f33a33e661/README.yaml @@ -58,9 +58,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 801 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD/GB3 (75:11:11:4) bilayer at 310 K (CHARMM36m, GROMACS, 7255 ns) [NMRlipids simulation 801] + name: Molecular dynamics trajectory of a POPC/CLA/SOD/GB3 (75:11:11:4) bilayer at + 310 K (CHARMM36m, GROMACS, 7255 ns) [NMRlipids simulation 801] alternateName: Gb3inPOPC_run1 - description: Molecular dynamics trajectory of a lipid bilayer of 190 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 75 mol%), 27 CLA (11 mol%), 27 SOD (11 mol%) and 10 GB3 (Gb3(d18:1/24:0), 4 mol%) at 310 K. Simulated with CHARMM36m in GROMACS for 7255 ns (74381 atoms). Deposited as NMRlipids Databank simulation 801 and available from https://doi.org/10.5281/zenodo.10635871. + description: Molecular dynamics trajectory of a lipid bilayer of 190 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 75 mol%), 27 CLA (11 mol%), 27 SOD (11 mol%) and 10 GB3 (Gb3(d18:1/24:0), 4 mol%) + at 310 K. Simulated with CHARMM36m in GROMACS for 7255 ns (74381 atoms). Deposited + as NMRlipids Databank simulation 801 and available from https://doi.org/10.5281/zenodo.10635871. sameAs: https://doi.org/10.5281/zenodo.10635871 datePublished: '2024-02-08' license: diff --git a/Simulations/832/d9e/832d9e9dd418287d709cfcf5aa8c8fc7bef98c2e/b3bfd314c993a94a13f4a5ac30acc1a26eda8096/README.yaml b/Simulations/832/d9e/832d9e9dd418287d709cfcf5aa8c8fc7bef98c2e/b3bfd314c993a94a13f4a5ac30acc1a26eda8096/README.yaml index 16b3e09f29..df5a448c5e 100644 --- a/Simulations/832/d9e/832d9e9dd418287d709cfcf5aa8c8fc7bef98c2e/b3bfd314c993a94a13f4a5ac30acc1a26eda8096/README.yaml +++ b/Simulations/832/d9e/832d9e9dd418287d709cfcf5aa8c8fc7bef98c2e/b3bfd314c993a94a13f4a5ac30acc1a26eda8096/README.yaml @@ -55,9 +55,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 45 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/CLA/SOD/DCHOL (74:9:9:9) bilayer at 310 K (Slipids, GROMACS, 700 ns) [NMRlipids simulation 45] + name: Molecular dynamics trajectory of a DPPC/CLA/SOD/DCHOL (74:9:9:9) bilayer at + 310 K (Slipids, GROMACS, 700 ns) [NMRlipids simulation 45] alternateName: 1032DPPC_120DCHOL_46440SOL_124SOD_124CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 1032 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 74 mol%), 124 CLA (9 mol%), 124 SOD (9 mol%) and 120 DCHOL (18,19-di-nor-cholesterol, 9 mol%) at 310 K. Simulated with Slipids in GROMACS for 700 ns (281888 atoms). Deposited as NMRlipids Databank simulation 45 and available from https://doi.org/10.5281/zenodo.3540513. + description: Molecular dynamics trajectory of a lipid bilayer of 1032 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 74 mol%), 124 CLA (9 mol%), 124 SOD (9 mol%) and 120 DCHOL (18,19-di-nor-cholesterol, + 9 mol%) at 310 K. Simulated with Slipids in GROMACS for 700 ns (281888 atoms). + Deposited as NMRlipids Databank simulation 45 and available from https://doi.org/10.5281/zenodo.3540513. sameAs: https://doi.org/10.5281/zenodo.3540513 datePublished: '2019-11-13' license: diff --git a/Simulations/833/b9c/833b9caa5aa455eacae414e4504f479a9b6949bb/bfb99c2b9c154a92eddcb25c4a888797823daaf6/README.yaml b/Simulations/833/b9c/833b9caa5aa455eacae414e4504f479a9b6949bb/bfb99c2b9c154a92eddcb25c4a888797823daaf6/README.yaml index d4de0bb00f..86547832a4 100644 --- a/Simulations/833/b9c/833b9caa5aa455eacae414e4504f479a9b6949bb/bfb99c2b9c154a92eddcb25c4a888797823daaf6/README.yaml +++ b/Simulations/833/b9c/833b9caa5aa455eacae414e4504f479a9b6949bb/bfb99c2b9c154a92eddcb25c4a888797823daaf6/README.yaml @@ -50,9 +50,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 114 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPS/POT (71:14:14) bilayer at 298 K (CHARMM36, GROMACS, 100 ns) [NMRlipids simulation 114] + name: Molecular dynamics trajectory of a POPC/POPS/POT (71:14:14) bilayer at 298 + K (CHARMM36, GROMACS, 100 ns) [NMRlipids simulation 114] alternateName: 110POPC_22POPS_22POT_4620SOL_298K_v1 - description: Molecular dynamics trajectory of a lipid bilayer of 110 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 71 mol%), 22 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 14 mol%) and 22 POT (14 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for 100 ns (31416 atoms). Deposited as NMRlipids Databank simulation 114 and available from https://doi.org/10.5281/zenodo.1182658. + description: Molecular dynamics trajectory of a lipid bilayer of 110 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 71 mol%), 22 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 14 mol%) + and 22 POT (14 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for 100 ns (31416 + atoms). Deposited as NMRlipids Databank simulation 114 and available from https://doi.org/10.5281/zenodo.1182658. sameAs: https://doi.org/10.5281/zenodo.1182658 datePublished: '2018-02-21' license: @@ -140,7 +144,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1182658 identifier: 10.5281/zenodo.1182658 url: https://doi.org/10.5281/zenodo.1182658 - name: Charmm36 Pops/Popc Simulations (Versions 1 And 2) 298 K 1.0 Nm Lj Switching With K Ions + name: Charmm36 Pops/Popc Simulations (Versions 1 And 2) 298 K 1.0 Nm Lj Switching + With K Ions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/835/bce/835bcec0015e9d4c0baccb7ed2136ad93ef6bea0/b3dab948513c6e029437b02df08da39d8b492ddd/README.yaml b/Simulations/835/bce/835bcec0015e9d4c0baccb7ed2136ad93ef6bea0/b3dab948513c6e029437b02df08da39d8b492ddd/README.yaml index 4e2013dd48..7d279ec096 100644 --- a/Simulations/835/bce/835bcec0015e9d4c0baccb7ed2136ad93ef6bea0/b3dab948513c6e029437b02df08da39d8b492ddd/README.yaml +++ b/Simulations/835/bce/835bcec0015e9d4c0baccb7ed2136ad93ef6bea0/b3dab948513c6e029437b02df08da39d8b492ddd/README.yaml @@ -43,9 +43,12 @@ EXPERIMENT: PYPC: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a PYPC bilayer at 333.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 628] + name: Molecular dynamics trajectory of a PYPC bilayer at 333.15 K (CHARMM36, GROMACS, + 1001 ns) [NMRlipids simulation 628] alternateName: 64PYPC_3200SOL_333K - description: Molecular dynamics trajectory of a lipid bilayer of 64 PYPC (1-(16:0)-2-(16:1$^\Delta9$)-sn-glycero-3-phosphocholine) at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (17792 atoms). Deposited as NMRlipids Databank simulation 628 and available from https://doi.org/10.5281/zenodo.6943413. + description: Molecular dynamics trajectory of a lipid bilayer of 64 PYPC (1-(16:0)-2-(16:1$^\Delta9$)-sn-glycero-3-phosphocholine) + at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (17792 atoms). Deposited + as NMRlipids Databank simulation 628 and available from https://doi.org/10.5281/zenodo.6943413. sameAs: https://doi.org/10.5281/zenodo.6943413 datePublished: '2022-07-30' license: @@ -133,7 +136,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.6943413 identifier: 10.5281/zenodo.6943413 url: https://doi.org/10.5281/zenodo.6943413 - name: Simulations of different single-component bilayers, three different system sizes + name: Simulations of different single-component bilayers, three different system + sizes publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/83c/c57/83cc57bab873a149632aa4480e2e6e62894946ca/3cdc7f3092e745c4ab1a381a72a6daa64df0a555/README.yaml b/Simulations/83c/c57/83cc57bab873a149632aa4480e2e6e62894946ca/3cdc7f3092e745c4ab1a381a72a6daa64df0a555/README.yaml index 6c0ae424cc..cf1df91035 100644 --- a/Simulations/83c/c57/83cc57bab873a149632aa4480e2e6e62894946ca/3cdc7f3092e745c4ab1a381a72a6daa64df0a555/README.yaml +++ b/Simulations/83c/c57/83cc57bab873a149632aa4480e2e6e62894946ca/3cdc7f3092e745c4ab1a381a72a6daa64df0a555/README.yaml @@ -65,9 +65,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 827 bioschema_properties: - name: Molecular dynamics trajectory of a TMA/BOG/TMCL/CLA/SOD (49:24:24:1:1) bilayer at 303.15 K (Charmm36, GROMACS 2023.2, 500 ns) [NMRlipids simulation 827] + name: Molecular dynamics trajectory of a TMA/BOG/TMCL/CLA/SOD (49:24:24:1:1) bilayer + at 303.15 K (Charmm36, GROMACS 2023.2, 500 ns) [NMRlipids simulation 827] alternateName: TMCL_BOG_TMA_NaCl_T303_21w/P - description: Molecular dynamics trajectory of a lipid bilayer of 160 TMA (49 mol%), 80 BOG (beta-octyl D-glucopyranoside, 24 mol%), 80 TMCL (Tetramyristoyl cardiolipin, 24 mol%), 4 CLA (1 mol%) and 4 SOD (1 mol%) at 303.15 K. Simulated with Charmm36 in GROMACS 2023.2 for 500 ns (38388 atoms). Deposited as NMRlipids Databank simulation 827 and available from https://doi.org/10.5281/zenodo.13981147. + description: Molecular dynamics trajectory of a lipid bilayer of 160 TMA (49 mol%), + 80 BOG (beta-octyl D-glucopyranoside, 24 mol%), 80 TMCL (Tetramyristoyl cardiolipin, + 24 mol%), 4 CLA (1 mol%) and 4 SOD (1 mol%) at 303.15 K. Simulated with Charmm36 + in GROMACS 2023.2 for 500 ns (38388 atoms). Deposited as NMRlipids Databank simulation + 827 and available from https://doi.org/10.5281/zenodo.13981147. sameAs: https://doi.org/10.5281/zenodo.13981147 datePublished: '2024-10-23' license: diff --git a/Simulations/849/742/849742b3e44d7549e5a42101d6694c171dbb2402/19918e691863c1e68796851450e534f4371c74cf/README.yaml b/Simulations/849/742/849742b3e44d7549e5a42101d6694c171dbb2402/19918e691863c1e68796851450e534f4371c74cf/README.yaml index cbae1b3b00..87a8376fec 100644 --- a/Simulations/849/742/849742b3e44d7549e5a42101d6694c171dbb2402/19918e691863c1e68796851450e534f4371c74cf/README.yaml +++ b/Simulations/849/742/849742b3e44d7549e5a42101d6694c171dbb2402/19918e691863c1e68796851450e534f4371c74cf/README.yaml @@ -54,9 +54,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 19 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/CLA/SOD (82:9:9) bilayer at 323 K (OPLSAA-compatible Berger-DPPC-06, GROMACS 4.6.7, 120 ns) [NMRlipids simulation 19] + name: Molecular dynamics trajectory of a DPPC/CLA/SOD (82:9:9) bilayer at 323 K + (OPLSAA-compatible Berger-DPPC-06, GROMACS 4.6.7, 120 ns) [NMRlipids simulation + 19] alternateName: 72DPPC_2864SOL_8SOD_8CLA_323K - description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 82 mol%), 8 CLA (9 mol%) and 8 SOD (9 mol%) at 323 K. Simulated with OPLSAA-compatible Berger-DPPC-06 in GROMACS 4.6.7 for 120 ns (12208 atoms). Deposited as NMRlipids Databank simulation 19 and available from https://doi.org/10.5281/zenodo.16485. + description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 82 mol%), 8 CLA (9 mol%) and 8 SOD (9 mol%) at 323 K. Simulated with OPLSAA-compatible + Berger-DPPC-06 in GROMACS 4.6.7 for 120 ns (12208 atoms). Deposited as NMRlipids + Databank simulation 19 and available from https://doi.org/10.5281/zenodo.16485. sameAs: https://doi.org/10.5281/zenodo.16485 datePublished: '2015-03-30' license: diff --git a/Simulations/84e/730/84e730ce5fc952714f30b3fad9f9a12d72579fcb/8bc3a15b282f4b28f49e40cb5a55e15d5e8b1a00/README.yaml b/Simulations/84e/730/84e730ce5fc952714f30b3fad9f9a12d72579fcb/8bc3a15b282f4b28f49e40cb5a55e15d5e8b1a00/README.yaml index b9413a1733..20ed3e21fd 100644 --- a/Simulations/84e/730/84e730ce5fc952714f30b3fad9f9a12d72579fcb/8bc3a15b282f4b28f49e40cb5a55e15d5e8b1a00/README.yaml +++ b/Simulations/84e/730/84e730ce5fc952714f30b3fad9f9a12d72579fcb/8bc3a15b282f4b28f49e40cb5a55e15d5e8b1a00/README.yaml @@ -55,9 +55,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 201 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL/CHOL (45:33:17:5) bilayer at 310.15 K (CHARMM36, GROMACS 5.0, 2000 ns) [NMRlipids simulation 201] + name: Molecular dynamics trajectory of a POPC/CLA/CAL/CHOL (45:33:17:5) bilayer + at 310.15 K (CHARMM36, GROMACS 5.0, 2000 ns) [NMRlipids simulation 201] alternateName: 22CHOL_200POPC_9000SOL_73CAL_146CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 45 mol%), 146 CLA (33 mol%), 73 CAL (17 mol%) and 22 CHOL (cholesterol, 5 mol%) at 310.15 K. Simulated with CHARMM36 in GROMACS 5.0 for 2000 ns (55647 atoms). Deposited as NMRlipids Databank simulation 201 and available from https://doi.org/10.5281/zenodo.259365. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 45 mol%), 146 CLA (33 mol%), 73 CAL (17 mol%) and 22 CHOL (cholesterol, 5 mol%) + at 310.15 K. Simulated with CHARMM36 in GROMACS 5.0 for 2000 ns (55647 atoms). + Deposited as NMRlipids Databank simulation 201 and available from https://doi.org/10.5281/zenodo.259365. sameAs: https://doi.org/10.5281/zenodo.259365 datePublished: '2017-01-24' license: @@ -147,7 +151,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.259365 identifier: 10.5281/zenodo.259365 url: https://doi.org/10.5281/zenodo.259365 - name: Popc With Varying Amounts Of Cholesterol, 450 Mm Of Cacl_2. Charmm36 With Default Charmm Ions + name: Popc With Varying Amounts Of Cholesterol, 450 Mm Of Cacl_2. Charmm36 With + Default Charmm Ions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/856/6fe/8566fe9ecc32415f1f3fe1b3ce8b4ef4f9b19a67/e022e9e0356a441dfd862555f70f576fdf640c8b/README.yaml b/Simulations/856/6fe/8566fe9ecc32415f1f3fe1b3ce8b4ef4f9b19a67/e022e9e0356a441dfd862555f70f576fdf640c8b/README.yaml index 633f8c1d03..d201f120f9 100644 --- a/Simulations/856/6fe/8566fe9ecc32415f1f3fe1b3ce8b4ef4f9b19a67/e022e9e0356a441dfd862555f70f576fdf640c8b/README.yaml +++ b/Simulations/856/6fe/8566fe9ecc32415f1f3fe1b3ce8b4ef4f9b19a67/e022e9e0356a441dfd862555f70f576fdf640c8b/README.yaml @@ -50,9 +50,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/8 ID: 661 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (62:38) bilayer at 298.15 K (Slipids, GROMACS 2021, 1001 ns) [NMRlipids simulation 661] + name: Molecular dynamics trajectory of a POPC/CHOL (62:38) bilayer at 298.15 K (Slipids, + GROMACS 2021, 1001 ns) [NMRlipids simulation 661] alternateName: Slipids_POPC_CHOL38_S - description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 62 mol%) and 40 CHOL (cholesterol, 38 mol%) at 298.15 K. Simulated with Slipids in GROMACS 2021 for 1001 ns (27136 atoms). Deposited as NMRlipids Databank simulation 661 and available from https://doi.org/10.5281/zenodo.7022749. + description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 62 mol%) and 40 CHOL (cholesterol, 38 mol%) at 298.15 K. Simulated with Slipids + in GROMACS 2021 for 1001 ns (27136 atoms). Deposited as NMRlipids Databank simulation + 661 and available from https://doi.org/10.5281/zenodo.7022749. sameAs: https://doi.org/10.5281/zenodo.7022749 datePublished: '2022-08-23' license: diff --git a/Simulations/861/c33/861c3389e16a8b84c2c581eea947b392d6a9da6a/861c3389e16a8b84c2c581eea947b392d6a9da6a/README.yaml b/Simulations/861/c33/861c3389e16a8b84c2c581eea947b392d6a9da6a/861c3389e16a8b84c2c581eea947b392d6a9da6a/README.yaml index c4439dfdc8..b04c261764 100644 --- a/Simulations/861/c33/861c3389e16a8b84c2c581eea947b392d6a9da6a/861c3389e16a8b84c2c581eea947b392d6a9da6a/README.yaml +++ b/Simulations/861/c33/861c3389e16a8b84c2c581eea947b392d6a9da6a/861c3389e16a8b84c2c581eea947b392d6a9da6a/README.yaml @@ -45,9 +45,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 736 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (45:37:18) bilayer at 303 K (Charmm-Drude polarizable; system has been equilibriated using Charmm36, OPENMM 7.4.1, 516 ns) [NMRlipids simulation 736] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (45:37:18) bilayer at 303 + K (Charmm-Drude polarizable; system has been equilibriated using Charmm36, OPENMM + 7.4.1, 516 ns) [NMRlipids simulation 736] alternateName: 128POPC_6400SOL_52CaCl2_303K - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 45 mol%), 104 CLA (37 mol%) and 52 CAL (18 mol%) at 303 K. Simulated with Charmm-Drude polarizable; system has been equilibriated using Charmm36 in OPENMM 7.4.1 for 516 ns (57144 atoms). Deposited as NMRlipids Databank simulation 736 and available from https://doi.org/10.5281/zenodo.7605016. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 45 mol%), 104 CLA (37 mol%) and 52 CAL (18 mol%) at 303 K. Simulated with Charmm-Drude + polarizable; system has been equilibriated using Charmm36 in OPENMM 7.4.1 for + 516 ns (57144 atoms). Deposited as NMRlipids Databank simulation 736 and available + from https://doi.org/10.5281/zenodo.7605016. sameAs: https://doi.org/10.5281/zenodo.7605016 datePublished: '2020-08-21' license: @@ -139,7 +145,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.7605016 identifier: 10.5281/zenodo.7605016 url: https://doi.org/10.5281/zenodo.7605016 - name: Pure POPC Membrane with 450mM CaCl2 simulations using Drude Polarizable Force Field and OpenMM + name: Pure POPC Membrane with 450mM CaCl2 simulations using Drude Polarizable + Force Field and OpenMM publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/866/0e5/8660e5ac104d11ad43c7f91c8cc940d393acbb1c/d1426c8f45fef51613ed55d87d58f791c346b4f2/README.yaml b/Simulations/866/0e5/8660e5ac104d11ad43c7f91c8cc940d393acbb1c/d1426c8f45fef51613ed55d87d58f791c346b4f2/README.yaml index af0e67c084..d50df8beaa 100644 --- a/Simulations/866/0e5/8660e5ac104d11ad43c7f91c8cc940d393acbb1c/d1426c8f45fef51613ed55d87d58f791c346b4f2/README.yaml +++ b/Simulations/866/0e5/8660e5ac104d11ad43c7f91c8cc940d393acbb1c/d1426c8f45fef51613ed55d87d58f791c346b4f2/README.yaml @@ -53,9 +53,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 484 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (88:8:4) bilayer at 310 K (CHARMM36 NBFIX Kim, GROMACS, 875 ns) [NMRlipids simulation 484] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (88:8:4) bilayer at 310 K + (CHARMM36 NBFIX Kim, GROMACS, 875 ns) [NMRlipids simulation 484] alternateName: 200POPC_9000SOL_9CAL_18CLA_310K_NBFIXKim - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 88 mol%), 18 CLA (8 mol%) and 9 CAL (4 mol%) at 310 K. Simulated with CHARMM36 NBFIX Kim in GROMACS for 875 ns (53827 atoms). Deposited as NMRlipids Databank simulation 484 and available from https://doi.org/10.5281/zenodo.3434396. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 88 mol%), 18 CLA (8 mol%) and 9 CAL (4 mol%) at 310 K. Simulated with CHARMM36 + NBFIX Kim in GROMACS for 875 ns (53827 atoms). Deposited as NMRlipids Databank + simulation 484 and available from https://doi.org/10.5281/zenodo.3434396. sameAs: https://doi.org/10.5281/zenodo.3434396 datePublished: '2019-09-17' license: diff --git a/Simulations/86a/f7e/86af7e0446c1bcdbd30766871258b65093351a12/ac10be8aa0a31d1bf48ac7a4400a75adb71008eb/README.yaml b/Simulations/86a/f7e/86af7e0446c1bcdbd30766871258b65093351a12/ac10be8aa0a31d1bf48ac7a4400a75adb71008eb/README.yaml index eae4bfd3bd..f8fa73206a 100644 --- a/Simulations/86a/f7e/86af7e0446c1bcdbd30766871258b65093351a12/ac10be8aa0a31d1bf48ac7a4400a75adb71008eb/README.yaml +++ b/Simulations/86a/f7e/86af7e0446c1bcdbd30766871258b65093351a12/ac10be8aa0a31d1bf48ac7a4400a75adb71008eb/README.yaml @@ -49,9 +49,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 567 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/CLA/SOD (82:9:9) bilayer at 310 K (Slipids, GROMACS 4.6, 300 ns) [NMRlipids simulation 567] + name: Molecular dynamics trajectory of a DPPC/CLA/SOD (82:9:9) bilayer at 310 K + (Slipids, GROMACS 4.6, 300 ns) [NMRlipids simulation 567] alternateName: 1152DPPC_46440SOL_124SOD_124CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 1152 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 82 mol%), 124 CLA (9 mol%) and 124 SOD (9 mol%) at 310 K. Simulated with Slipids in GROMACS 4.6 for 300 ns (289328 atoms). Deposited as NMRlipids Databank simulation 567 and available from https://doi.org/10.5281/zenodo.439080. + description: Molecular dynamics trajectory of a lipid bilayer of 1152 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 82 mol%), 124 CLA (9 mol%) and 124 SOD (9 mol%) at 310 K. Simulated with Slipids + in GROMACS 4.6 for 300 ns (289328 atoms). Deposited as NMRlipids Databank simulation + 567 and available from https://doi.org/10.5281/zenodo.439080. sameAs: https://doi.org/10.5281/zenodo.439080 datePublished: '2017-03-29' license: @@ -143,7 +147,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.439080 identifier: 10.5281/zenodo.439080 url: https://doi.org/10.5281/zenodo.439080 - name: Simulations Of Dppc/Cholesterol Bilayers With The Slipids Force Field, Part 2/2 + name: Simulations Of Dppc/Cholesterol Bilayers With The Slipids Force Field, Part + 2/2 publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/874/256/87425634a08154ef405aea238908c2891031d54c/17afdd19e48164c2b201d4cc9bfef1ccf06cd281/README.yaml b/Simulations/874/256/87425634a08154ef405aea238908c2891031d54c/17afdd19e48164c2b201d4cc9bfef1ccf06cd281/README.yaml index 88be6a9eee..0cc03850af 100644 --- a/Simulations/874/256/87425634a08154ef405aea238908c2891031d54c/17afdd19e48164c2b201d4cc9bfef1ccf06cd281/README.yaml +++ b/Simulations/874/256/87425634a08154ef405aea238908c2891031d54c/17afdd19e48164c2b201d4cc9bfef1ccf06cd281/README.yaml @@ -43,9 +43,12 @@ TRJLENGTH: 100010.0 DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 416 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 310 K (CHARMM36, GROMACS, 100 ns) [NMRlipids simulation 416] + name: Molecular dynamics trajectory of a POPC bilayer at 310 K (CHARMM36, GROMACS, + 100 ns) [NMRlipids simulation 416] alternateName: POPC_T310K - description: Molecular dynamics trajectory of a lipid bilayer of 500 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 310 K. Simulated with CHARMM36 in GROMACS for 100 ns (142000 atoms). Deposited as NMRlipids Databank simulation 416 and available from https://doi.org/10.5281/zenodo.3247813. + description: Molecular dynamics trajectory of a lipid bilayer of 500 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 310 K. Simulated with CHARMM36 in GROMACS for 100 ns (142000 atoms). Deposited + as NMRlipids Databank simulation 416 and available from https://doi.org/10.5281/zenodo.3247813. sameAs: https://doi.org/10.5281/zenodo.3247813 datePublished: '2019-06-17' license: diff --git a/Simulations/87f/d72/87fd72d7d0b20475b8ed3656dcdde54edba77f5e/0cf7b5e72d653004a8996d04c5d6066b26310a5e/README.yaml b/Simulations/87f/d72/87fd72d7d0b20475b8ed3656dcdde54edba77f5e/0cf7b5e72d653004a8996d04c5d6066b26310a5e/README.yaml index 7068d58f2e..cfe4f3025b 100644 --- a/Simulations/87f/d72/87fd72d7d0b20475b8ed3656dcdde54edba77f5e/0cf7b5e72d653004a8996d04c5d6066b26310a5e/README.yaml +++ b/Simulations/87f/d72/87fd72d7d0b20475b8ed3656dcdde54edba77f5e/0cf7b5e72d653004a8996d04c5d6066b26310a5e/README.yaml @@ -55,9 +55,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 152 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD/CHOL (33:27:27:14) bilayer at 310 K (Slipids with ions by Smith & Dang, GROMACS 4.6, 200 ns) [NMRlipids simulation 152] + name: Molecular dynamics trajectory of a POPC/CLA/SOD/CHOL (33:27:27:14) bilayer + at 310 K (Slipids with ions by Smith & Dang, GROMACS 4.6, 200 ns) [NMRlipids simulation + 152] alternateName: 86CHOL_200POPC_9000SOL_162SOD_162CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 33 mol%), 162 CLA (27 mol%), 162 SOD (27 mol%) and 86 CHOL (cholesterol, 14 mol%) at 310 K. Simulated with Slipids with ions by Smith & Dang in GROMACS 4.6 for 200 ns (60488 atoms). Deposited as NMRlipids Databank simulation 152 and available from https://doi.org/10.5281/zenodo.259341. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 33 mol%), 162 CLA (27 mol%), 162 SOD (27 mol%) and 86 CHOL (cholesterol, 14 mol%) + at 310 K. Simulated with Slipids with ions by Smith & Dang in GROMACS 4.6 for + 200 ns (60488 atoms). Deposited as NMRlipids Databank simulation 152 and available + from https://doi.org/10.5281/zenodo.259341. sameAs: https://doi.org/10.5281/zenodo.259341 datePublished: '2017-01-24' license: @@ -147,7 +153,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.259341 identifier: 10.5281/zenodo.259341 url: https://doi.org/10.5281/zenodo.259341 - name: Popc With Varying Amounts Of Cholesterol, 1 M Of Nacl. Slipids With Ions By Smith & Dang + name: Popc With Varying Amounts Of Cholesterol, 1 M Of Nacl. Slipids With Ions + By Smith & Dang publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/880/982/880982b4fb12755f33c908acf5a7a023eb3f4a30/8858fd6be09953b0c30dc8bd155e811fb66d238a/README.yaml b/Simulations/880/982/880982b4fb12755f33c908acf5a7a023eb3f4a30/8858fd6be09953b0c30dc8bd155e811fb66d238a/README.yaml index 9714cb3c08..6698fa137b 100644 --- a/Simulations/880/982/880982b4fb12755f33c908acf5a7a023eb3f4a30/8858fd6be09953b0c30dc8bd155e811fb66d238a/README.yaml +++ b/Simulations/880/982/880982b4fb12755f33c908acf5a7a023eb3f4a30/8858fd6be09953b0c30dc8bd155e811fb66d238a/README.yaml @@ -50,9 +50,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 845 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (79:14:7) bilayer at 310 K (CHARMM36, GROMACS, 1000 ns) [NMRlipids simulation 845] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (79:14:7) bilayer at 310 K + (CHARMM36, GROMACS, 1000 ns) [NMRlipids simulation 845] alternateName: POPC_113mM_CaCl_CHARMM36 - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 79 mol%), 36 CLA (14 mol%) and 18 CAL (7 mol%) at 310 K. Simulated with CHARMM36 in GROMACS for 1000 ns (53854 atoms). Deposited as NMRlipids Databank simulation 845 and available from https://doi.org/10.5281/zenodo.10464946. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 79 mol%), 36 CLA (14 mol%) and 18 CAL (7 mol%) at 310 K. Simulated with CHARMM36 + in GROMACS for 1000 ns (53854 atoms). Deposited as NMRlipids Databank simulation + 845 and available from https://doi.org/10.5281/zenodo.10464946. sameAs: https://doi.org/10.5281/zenodo.10464946 datePublished: '2024-01-06' license: diff --git a/Simulations/887/8ed/8878edf15de4f14d50277f8ba2a5d77d0a58c860/8878edf15de4f14d50277f8ba2a5d77d0a58c860/README.yaml b/Simulations/887/8ed/8878edf15de4f14d50277f8ba2a5d77d0a58c860/8878edf15de4f14d50277f8ba2a5d77d0a58c860/README.yaml index 0a3ad2432b..759d56a6a7 100644 --- a/Simulations/887/8ed/8878edf15de4f14d50277f8ba2a5d77d0a58c860/8878edf15de4f14d50277f8ba2a5d77d0a58c860/README.yaml +++ b/Simulations/887/8ed/8878edf15de4f14d50277f8ba2a5d77d0a58c860/8878edf15de4f14d50277f8ba2a5d77d0a58c860/README.yaml @@ -38,9 +38,12 @@ EXPERIMENT: FORMFACTOR: - 10.1016/j.chemphyslip.2020.104892/2 bioschema_properties: - name: Molecular dynamics trajectory of a SDPC bilayer at 303.15 K (CHARMM36m, NAMD 3, 500 ns) [NMRlipids simulation 894] + name: Molecular dynamics trajectory of a SDPC bilayer at 303.15 K (CHARMM36m, NAMD + 3, 500 ns) [NMRlipids simulation 894] alternateName: SDPC - description: Molecular dynamics trajectory of a lipid bilayer of 200 SDPC (1-stearoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine) at 303.15 K. Simulated with CHARMM36m in NAMD 3 for 500 ns (56000 atoms). Deposited as NMRlipids Databank simulation 894 and available from https://doi.org/10.5281/zenodo.18384813. + description: Molecular dynamics trajectory of a lipid bilayer of 200 SDPC (1-stearoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine) + at 303.15 K. Simulated with CHARMM36m in NAMD 3 for 500 ns (56000 atoms). Deposited + as NMRlipids Databank simulation 894 and available from https://doi.org/10.5281/zenodo.18384813. sameAs: https://doi.org/10.5281/zenodo.18384813 datePublished: '2026-01-27' license: @@ -132,7 +135,9 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.18384813 identifier: 10.5281/zenodo.18384813 url: https://doi.org/10.5281/zenodo.18384813 - name: Polyunsaturated 1-stearoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine (18:0/22:6) | SDPC lipid bilayer, 303K, CHARMM36m-WYF forcefield, NAMD 3.0.2, 2* 500 ns + name: Polyunsaturated 1-stearoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine + (18:0/22:6) | SDPC lipid bilayer, 303K, CHARMM36m-WYF forcefield, NAMD 3.0.2, + 2* 500 ns publisher: Zenodo _source: api: datacite diff --git a/Simulations/888/c03/888c031cd88bd97a5584a120dee76bf673e438ff/369daa4fed207d6e3d3199466c3f260535334f11/README.yaml b/Simulations/888/c03/888c031cd88bd97a5584a120dee76bf673e438ff/369daa4fed207d6e3d3199466c3f260535334f11/README.yaml index 34180123e7..ae5a27acec 100644 --- a/Simulations/888/c03/888c031cd88bd97a5584a120dee76bf673e438ff/369daa4fed207d6e3d3199466c3f260535334f11/README.yaml +++ b/Simulations/888/c03/888c031cd88bd97a5584a120dee76bf673e438ff/369daa4fed207d6e3d3199466c3f260535334f11/README.yaml @@ -39,9 +39,12 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 357 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC bilayer at 288 K (CHARMM36, GROMACS 2020, 25 ns) [NMRlipids simulation 357] + name: Molecular dynamics trajectory of a DPPC bilayer at 288 K (CHARMM36, GROMACS + 2020, 25 ns) [NMRlipids simulation 357] alternateName: 192DPPC_318692SOL_288K - description: Molecular dynamics trajectory of a lipid bilayer of 256 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) at 288 K. Simulated with CHARMM36 in GROMACS 2020 for 25 ns (160756 atoms). Deposited as NMRlipids Databank simulation 357 and available from https://doi.org/10.5281/zenodo.4300706. + description: Molecular dynamics trajectory of a lipid bilayer of 256 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) + at 288 K. Simulated with CHARMM36 in GROMACS 2020 for 25 ns (160756 atoms). Deposited + as NMRlipids Databank simulation 357 and available from https://doi.org/10.5281/zenodo.4300706. sameAs: https://doi.org/10.5281/zenodo.4300706 datePublished: '2020-12-01' license: @@ -134,7 +137,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.4300706 identifier: 10.5281/zenodo.4300706 url: https://doi.org/10.5281/zenodo.4300706 - name: 256 DPPC Molecules bilayer in pure Water, simulated at 288K (gel) or 358K (fluid) + name: 256 DPPC Molecules bilayer in pure Water, simulated at 288K (gel) or 358K + (fluid) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/88c/02d/88c02d2e58d6c59918f230e060130570e398071e/32ba461564dfbf8212488be80ddf109e3de23c1f/README.yaml b/Simulations/88c/02d/88c02d2e58d6c59918f230e060130570e398071e/32ba461564dfbf8212488be80ddf109e3de23c1f/README.yaml index 0ae078c24c..6cb812ac12 100644 --- a/Simulations/88c/02d/88c02d2e58d6c59918f230e060130570e398071e/32ba461564dfbf8212488be80ddf109e3de23c1f/README.yaml +++ b/Simulations/88c/02d/88c02d2e58d6c59918f230e060130570e398071e/32ba461564dfbf8212488be80ddf109e3de23c1f/README.yaml @@ -47,9 +47,12 @@ EXPERIMENT: - 10.1016/j.bbamem.2011.07.022/19 ID: 501 bioschema_properties: - name: Molecular dynamics trajectory of a DMPC bilayer at 323 K (Berger, GROMACS 3.x, 110 ns) [NMRlipids simulation 501] + name: Molecular dynamics trajectory of a DMPC bilayer at 323 K (Berger, GROMACS + 3.x, 110 ns) [NMRlipids simulation 501] alternateName: 128DMPC_5097SOL_323K_Berger - description: Molecular dynamics trajectory of a lipid bilayer of 128 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) at 323 K. Simulated with Berger in GROMACS 3.x for 110 ns (21179 atoms). Deposited as NMRlipids Databank simulation 501 and available from https://doi.org/10.5281/zenodo.51635. + description: Molecular dynamics trajectory of a lipid bilayer of 128 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) + at 323 K. Simulated with Berger in GROMACS 3.x for 110 ns (21179 atoms). Deposited + as NMRlipids Databank simulation 501 and available from https://doi.org/10.5281/zenodo.51635. sameAs: https://doi.org/10.5281/zenodo.51635 datePublished: '2013-10-23' license: @@ -144,7 +147,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.51635 identifier: 10.5281/zenodo.51635 url: https://doi.org/10.5281/zenodo.51635 - name: Molecular dynamics simulation trajectory of a fully hydrated DMPC lipid bilayer + name: Molecular dynamics simulation trajectory of a fully hydrated DMPC lipid + bilayer publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/895/c8e/895c8ebafa41c32a750d104df7523d4f71088470/c3f3385efdfacf66ce7023fe653f18259af20c10/README.yaml b/Simulations/895/c8e/895c8ebafa41c32a750d104df7523d4f71088470/c3f3385efdfacf66ce7023fe653f18259af20c10/README.yaml index f9ca21d4bb..c4804237d1 100644 --- a/Simulations/895/c8e/895c8ebafa41c32a750d104df7523d4f71088470/c3f3385efdfacf66ce7023fe653f18259af20c10/README.yaml +++ b/Simulations/895/c8e/895c8ebafa41c32a750d104df7523d4f71088470/c3f3385efdfacf66ce7023fe653f18259af20c10/README.yaml @@ -56,9 +56,14 @@ SOFTWARE: gromacs DIR_WRK: /usr/home/bort/Databank ID: 251 bioschema_properties: - name: Molecular dynamics trajectory of a DOPC/DDOPC/CHOL (48:42:10) bilayer at 310 K (CHARMM36, GROMACS, 1000 ns) [NMRlipids simulation 251] + name: Molecular dynamics trajectory of a DOPC/DDOPC/CHOL (48:42:10) bilayer at 310 + K (CHARMM36, GROMACS, 1000 ns) [NMRlipids simulation 251] alternateName: 28CHOL_130DOPC_115DDOPC_10920SOL_310K - description: Molecular dynamics trajectory of a lipid bilayer of 130 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, 48 mol%), 115 DDOPC (1,2-didocosahexaenoyl-sn-glycero-3-phosphocholine, 42 mol%) and 28 CHOL (cholesterol, 10 mol%) at 310 K. Simulated with CHARMM36 in GROMACS for 1000 ns (69102 atoms). Deposited as NMRlipids Databank simulation 251 and available from https://doi.org/10.5281/zenodo.2653723. + description: Molecular dynamics trajectory of a lipid bilayer of 130 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, + 48 mol%), 115 DDOPC (1,2-didocosahexaenoyl-sn-glycero-3-phosphocholine, 42 mol%) + and 28 CHOL (cholesterol, 10 mol%) at 310 K. Simulated with CHARMM36 in GROMACS + for 1000 ns (69102 atoms). Deposited as NMRlipids Databank simulation 251 and + available from https://doi.org/10.5281/zenodo.2653723. sameAs: https://doi.org/10.5281/zenodo.2653723 datePublished: '2019-04-29' license: @@ -149,7 +154,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.2653723 identifier: 10.5281/zenodo.2653723 url: https://doi.org/10.5281/zenodo.2653723 - name: Atomistic simulations of cholesterol in asymmetric lipid bilayers with varying degrees of lipid chain unsaturation + name: Atomistic simulations of cholesterol in asymmetric lipid bilayers with varying + degrees of lipid chain unsaturation publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/89a/9a4/89a9a48c2494b41ea60988ceb5cf197564bb9b73/9d27707ef545963e0723252396311bfa590a7f5f/README.yaml b/Simulations/89a/9a4/89a9a48c2494b41ea60988ceb5cf197564bb9b73/9d27707ef545963e0723252396311bfa590a7f5f/README.yaml index 71ecd6767b..8df1f30182 100644 --- a/Simulations/89a/9a4/89a9a48c2494b41ea60988ceb5cf197564bb9b73/9d27707ef545963e0723252396311bfa590a7f5f/README.yaml +++ b/Simulations/89a/9a4/89a9a48c2494b41ea60988ceb5cf197564bb9b73/9d27707ef545963e0723252396311bfa590a7f5f/README.yaml @@ -49,9 +49,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 163 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (82:9:9) bilayer at 310 K (CHARMM36, GROMACS 5.0.4, 500 ns) [NMRlipids simulation 163] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (82:9:9) bilayer at 310 K + (CHARMM36, GROMACS 5.0.4, 500 ns) [NMRlipids simulation 163] alternateName: 512POPC_20480SOLtip3_55SOD_55CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 512 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 82 mol%), 55 CLA (9 mol%) and 55 SOD (9 mol%) at 310 K. Simulated with CHARMM36 in GROMACS 5.0.4 for 500 ns (130158 atoms). Deposited as NMRlipids Databank simulation 163 and available from https://doi.org/10.5281/zenodo.1010083. + description: Molecular dynamics trajectory of a lipid bilayer of 512 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 82 mol%), 55 CLA (9 mol%) and 55 SOD (9 mol%) at 310 K. Simulated with CHARMM36 + in GROMACS 5.0.4 for 500 ns (130158 atoms). Deposited as NMRlipids Databank simulation + 163 and available from https://doi.org/10.5281/zenodo.1010083. sameAs: https://doi.org/10.5281/zenodo.1010083 datePublished: '2017-10-12' license: diff --git a/Simulations/89b/b82/89bb82ff4c5bcbb37f09acfdc4eb3f5d42e1b5da/4079b7a4deb02e8f7571a6769aa2c23296e0f117/README.yaml b/Simulations/89b/b82/89bb82ff4c5bcbb37f09acfdc4eb3f5d42e1b5da/4079b7a4deb02e8f7571a6769aa2c23296e0f117/README.yaml index eadd3722e2..f48152f8b0 100644 --- a/Simulations/89b/b82/89bb82ff4c5bcbb37f09acfdc4eb3f5d42e1b5da/4079b7a4deb02e8f7571a6769aa2c23296e0f117/README.yaml +++ b/Simulations/89b/b82/89bb82ff4c5bcbb37f09acfdc4eb3f5d42e1b5da/4079b7a4deb02e8f7571a6769aa2c23296e0f117/README.yaml @@ -43,9 +43,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 396 bioschema_properties: - name: Molecular dynamics trajectory of a DOPC bilayer at 313.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 396] + name: Molecular dynamics trajectory of a DOPC bilayer at 313.15 K (CHARMM36, GROMACS, + 1001 ns) [NMRlipids simulation 396] alternateName: 64DOPC_3200SOL_313K - description: Molecular dynamics trajectory of a lipid bilayer of 64 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) at 313.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (18432 atoms). Deposited as NMRlipids Databank simulation 396 and available from https://doi.org/10.5281/zenodo.6943086. + description: Molecular dynamics trajectory of a lipid bilayer of 64 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) + at 313.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (18432 atoms). Deposited + as NMRlipids Databank simulation 396 and available from https://doi.org/10.5281/zenodo.6943086. sameAs: https://doi.org/10.5281/zenodo.6943086 datePublished: '2022-07-30' license: diff --git a/Simulations/89c/628/89c6286bdc3e222b3262562efa53e05c7d18f4dd/6dcc5d021a931c1114b231881bd9e957ce5670b3/README.yaml b/Simulations/89c/628/89c6286bdc3e222b3262562efa53e05c7d18f4dd/6dcc5d021a931c1114b231881bd9e957ce5670b3/README.yaml index 9b70e55c9c..1f0f8e372f 100644 --- a/Simulations/89c/628/89c6286bdc3e222b3262562efa53e05c7d18f4dd/6dcc5d021a931c1114b231881bd9e957ce5670b3/README.yaml +++ b/Simulations/89c/628/89c6286bdc3e222b3262562efa53e05c7d18f4dd/6dcc5d021a931c1114b231881bd9e957ce5670b3/README.yaml @@ -55,9 +55,14 @@ EXPERIMENT: SM16: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a POPC/SM16/ERG (40:40:20) bilayer at 295 K (Slipids, GROMACS 2019.6, 100 ns) [NMRlipids simulation 848] + name: Molecular dynamics trajectory of a POPC/SM16/ERG (40:40:20) bilayer at 295 + K (Slipids, GROMACS 2019.6, 100 ns) [NMRlipids simulation 848] alternateName: POPC/SM16/ERG(2:2:1) - description: Molecular dynamics trajectory of a lipid bilayer of 408 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 40 mol%), 408 SM16 (N-palmitoyl-D-erythro-sphingosylphosphorylcholine, 40 mol%) and 208 ERG (ergosterol, 20 mol%) at 295 K. Simulated with Slipids in GROMACS 2019.6 for 100 ns (229192 atoms). Deposited as NMRlipids Databank simulation 848 and available from https://doi.org/10.5281/zenodo.17730115. + description: Molecular dynamics trajectory of a lipid bilayer of 408 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 40 mol%), 408 SM16 (N-palmitoyl-D-erythro-sphingosylphosphorylcholine, 40 mol%) + and 208 ERG (ergosterol, 20 mol%) at 295 K. Simulated with Slipids in GROMACS + 2019.6 for 100 ns (229192 atoms). Deposited as NMRlipids Databank simulation 848 + and available from https://doi.org/10.5281/zenodo.17730115. sameAs: https://doi.org/10.5281/zenodo.17730115 datePublished: '2025-11-26' license: @@ -151,7 +156,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.17730115 identifier: 10.5281/zenodo.17730115 url: https://doi.org/10.5281/zenodo.17730115 - name: 'MD simulation trajectory of Ternary mixture of POPC/PSM/Ergo (2:2:1) at 295 K: Slipids, GROMACS 2019.6' + name: 'MD simulation trajectory of Ternary mixture of POPC/PSM/Ergo (2:2:1) at + 295 K: Slipids, GROMACS 2019.6' publisher: Zenodo _source: api: datacite diff --git a/Simulations/89d/a41/89da414cb29d949f428fda5cb6b91a217fc25a37/00d3801d4ed021bc79b766e016586f9ad4d38232/README.yaml b/Simulations/89d/a41/89da414cb29d949f428fda5cb6b91a217fc25a37/00d3801d4ed021bc79b766e016586f9ad4d38232/README.yaml index e93aaabc52..c0b3febda2 100644 --- a/Simulations/89d/a41/89da414cb29d949f428fda5cb6b91a217fc25a37/00d3801d4ed021bc79b766e016586f9ad4d38232/README.yaml +++ b/Simulations/89d/a41/89da414cb29d949f428fda5cb6b91a217fc25a37/00d3801d4ed021bc79b766e016586f9ad4d38232/README.yaml @@ -49,9 +49,13 @@ WARNINGS: PBC: z-jumps ID: 369 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (84:16) bilayer at 303 K (Lipid14, GROMACS 5.0.4, 200 ns) [NMRlipids simulation 369] + name: Molecular dynamics trajectory of a POPC/CHOL (84:16) bilayer at 303 K (Lipid14, + GROMACS 5.0.4, 200 ns) [NMRlipids simulation 369] alternateName: 108POPC_20CHOL_3968SOL_303K - description: Molecular dynamics trajectory of a lipid bilayer of 108 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 84 mol%) and 20 CHOL (cholesterol, 16 mol%) at 303 K. Simulated with Lipid14 in GROMACS 5.0.4 for 200 ns (27856 atoms). Deposited as NMRlipids Databank simulation 369 and available from https://doi.org/10.5281/zenodo.3871000. + description: Molecular dynamics trajectory of a lipid bilayer of 108 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 84 mol%) and 20 CHOL (cholesterol, 16 mol%) at 303 K. Simulated with Lipid14 in + GROMACS 5.0.4 for 200 ns (27856 atoms). Deposited as NMRlipids Databank simulation + 369 and available from https://doi.org/10.5281/zenodo.3871000. sameAs: https://doi.org/10.5281/zenodo.3871000 datePublished: '2020-06-01' license: @@ -140,7 +144,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3871000 identifier: 10.5281/zenodo.3871000 url: https://doi.org/10.5281/zenodo.3871000 - name: 'MD simulations of bilayers containing POPC and Cholesterol: 108POPC_20CHL_31Nwat_neutral (lipid14)' + name: 'MD simulations of bilayers containing POPC and Cholesterol: 108POPC_20CHL_31Nwat_neutral + (lipid14)' publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/89f/028/89f02864694d0a95da32b640f639a5d9c6f75f87/a5f5bf3e63c6f5d5200b4375ddc742b4749a1ac7/README.yaml b/Simulations/89f/028/89f02864694d0a95da32b640f639a5d9c6f75f87/a5f5bf3e63c6f5d5200b4375ddc742b4749a1ac7/README.yaml index d449fd74f9..1e2f7981cd 100644 --- a/Simulations/89f/028/89f02864694d0a95da32b640f639a5d9c6f75f87/a5f5bf3e63c6f5d5200b4375ddc742b4749a1ac7/README.yaml +++ b/Simulations/89f/028/89f02864694d0a95da32b640f639a5d9c6f75f87/a5f5bf3e63c6f5d5200b4375ddc742b4749a1ac7/README.yaml @@ -44,9 +44,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 94 bioschema_properties: - name: Molecular dynamics trajectory of a DLPC bilayer at 300 K (Berger-DLPC-13, GROMACS 4.5.4, 80 ns) [NMRlipids simulation 94] + name: Molecular dynamics trajectory of a DLPC bilayer at 300 K (Berger-DLPC-13, + GROMACS 4.5.4, 80 ns) [NMRlipids simulation 94] alternateName: 72DLPC_576SOL_300K - description: Molecular dynamics trajectory of a lipid bilayer of 72 DLPC (1,2-dilauroyl-sn-glycero-3-phosphocholine) at 300 K. Simulated with Berger-DLPC-13 in GROMACS 4.5.4 for 80 ns (4752 atoms). Deposited as NMRlipids Databank simulation 94 and available from https://doi.org/10.5281/zenodo.16294. + description: Molecular dynamics trajectory of a lipid bilayer of 72 DLPC (1,2-dilauroyl-sn-glycero-3-phosphocholine) + at 300 K. Simulated with Berger-DLPC-13 in GROMACS 4.5.4 for 80 ns (4752 atoms). + Deposited as NMRlipids Databank simulation 94 and available from https://doi.org/10.5281/zenodo.16294. sameAs: https://doi.org/10.5281/zenodo.16294 datePublished: '2015-03-24' license: diff --git a/Simulations/8a3/b23/8a3b239ccdf049fa51ffef3b436541da170b0b29/9ddacfe8666c6c43d77985ec2dcf5fd6d49dd452/README.yaml b/Simulations/8a3/b23/8a3b239ccdf049fa51ffef3b436541da170b0b29/9ddacfe8666c6c43d77985ec2dcf5fd6d49dd452/README.yaml index 6a278bfc12..f75d657936 100644 --- a/Simulations/8a3/b23/8a3b239ccdf049fa51ffef3b436541da170b0b29/9ddacfe8666c6c43d77985ec2dcf5fd6d49dd452/README.yaml +++ b/Simulations/8a3/b23/8a3b239ccdf049fa51ffef3b436541da170b0b29/9ddacfe8666c6c43d77985ec2dcf5fd6d49dd452/README.yaml @@ -52,9 +52,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/9 ID: 704 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (53:47) bilayer at 298.15 K (MacRog, GROMACS 2021, 1001 ns) [NMRlipids simulation 704] + name: Molecular dynamics trajectory of a POPC/CHOL (53:47) bilayer at 298.15 K (MacRog, + GROMACS 2021, 1001 ns) [NMRlipids simulation 704] alternateName: MacRog_POPC_CHOL47_S - description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 53 mol%) and 56 CHOL (cholesterol, 47 mol%) at 298.15 K. Simulated with MacRog in GROMACS 2021 for 1001 ns (30720 atoms). Deposited as NMRlipids Databank simulation 704 and available from https://doi.org/10.5281/zenodo.7061800. + description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 53 mol%) and 56 CHOL (cholesterol, 47 mol%) at 298.15 K. Simulated with MacRog + in GROMACS 2021 for 1001 ns (30720 atoms). Deposited as NMRlipids Databank simulation + 704 and available from https://doi.org/10.5281/zenodo.7061800. sameAs: https://doi.org/10.5281/zenodo.7061800 datePublished: '2022-09-08' license: diff --git a/Simulations/8a4/d1e/8a4d1ef506194f34756b450fdb85cd25b2622685/42e758d0b36ac79a7cc9a8093dae1d79324d5f29/README.yaml b/Simulations/8a4/d1e/8a4d1ef506194f34756b450fdb85cd25b2622685/42e758d0b36ac79a7cc9a8093dae1d79324d5f29/README.yaml index 985c297b69..ba40cfba71 100644 --- a/Simulations/8a4/d1e/8a4d1ef506194f34756b450fdb85cd25b2622685/42e758d0b36ac79a7cc9a8093dae1d79324d5f29/README.yaml +++ b/Simulations/8a4/d1e/8a4d1ef506194f34756b450fdb85cd25b2622685/42e758d0b36ac79a7cc9a8093dae1d79324d5f29/README.yaml @@ -56,9 +56,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 306 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CHOL/CAL (40:29:17:14) bilayer at 310 K (Slipids with default Amber ions parameters (type C0), GROMACS 4.6, 2000 ns) [NMRlipids simulation 306] + name: Molecular dynamics trajectory of a POPC/CLA/CHOL/CAL (40:29:17:14) bilayer + at 310 K (Slipids with default Amber ions parameters (type C0), GROMACS 4.6, 2000 + ns) [NMRlipids simulation 306] alternateName: 86CHOL_200POPC_9000SOL_73CAL_146CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 40 mol%), 146 CLA (29 mol%), 86 CHOL (cholesterol, 17 mol%) and 73 CAL (14 mol%) at 310 K. Simulated with Slipids with default Amber ions parameters (type C0) in GROMACS 4.6 for 2000 ns (60383 atoms). Deposited as NMRlipids Databank simulation 306 and available from https://doi.org/10.5281/zenodo.259349. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 40 mol%), 146 CLA (29 mol%), 86 CHOL (cholesterol, 17 mol%) and 73 CAL (14 mol%) + at 310 K. Simulated with Slipids with default Amber ions parameters (type C0) + in GROMACS 4.6 for 2000 ns (60383 atoms). Deposited as NMRlipids Databank simulation + 306 and available from https://doi.org/10.5281/zenodo.259349. sameAs: https://doi.org/10.5281/zenodo.259349 datePublished: '2017-01-24' license: @@ -148,7 +154,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.259349 identifier: 10.5281/zenodo.259349 url: https://doi.org/10.5281/zenodo.259349 - name: Popc With Varying Amounts Of Cholesterol, 450 Mm Of Cacl_2. Slipids With Default Amber Ions + name: Popc With Varying Amounts Of Cholesterol, 450 Mm Of Cacl_2. Slipids With + Default Amber Ions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/8a9/8a7/8a98a788c0ba45e10d83d78839cf8d43d51f79cd/1d74dea696047a7160496ccfbb5f3a37ce288a24/README.yaml b/Simulations/8a9/8a7/8a98a788c0ba45e10d83d78839cf8d43d51f79cd/1d74dea696047a7160496ccfbb5f3a37ce288a24/README.yaml index c40ba9b37d..1b9601a2d2 100644 --- a/Simulations/8a9/8a7/8a98a788c0ba45e10d83d78839cf8d43d51f79cd/1d74dea696047a7160496ccfbb5f3a37ce288a24/README.yaml +++ b/Simulations/8a9/8a7/8a98a788c0ba45e10d83d78839cf8d43d51f79cd/1d74dea696047a7160496ccfbb5f3a37ce288a24/README.yaml @@ -61,9 +61,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 177 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL/POPS/SOD (49:21:11:10:10) bilayer at 298 K (Lipid17 and Dang ions, GROMACS 2018.0, 975 ns) [NMRlipids simulation 177] + name: Molecular dynamics trajectory of a POPC/CLA/CAL/POPS/SOD (49:21:11:10:10) + bilayer at 298 K (Lipid17 and Dang ions, GROMACS 2018.0, 975 ns) [NMRlipids simulation + 177] alternateName: 60POPC_12POPS_3561SOL_13CAL_26CLA_12SOD_298K - description: Molecular dynamics trajectory of a lipid bilayer of 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 49 mol%), 26 CLA (21 mol%), 13 CAL (11 mol%), 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 10 mol%) and 12 SOD (10 mol%) at 298 K. Simulated with Lipid17 and Dang ions in GROMACS 2018.0 for 975 ns (20298 atoms). Deposited as NMRlipids Databank simulation 177 and available from https://doi.org/10.5281/zenodo.1487761. + description: Molecular dynamics trajectory of a lipid bilayer of 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 49 mol%), 26 CLA (21 mol%), 13 CAL (11 mol%), 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, + 10 mol%) and 12 SOD (10 mol%) at 298 K. Simulated with Lipid17 and Dang ions in + GROMACS 2018.0 for 975 ns (20298 atoms). Deposited as NMRlipids Databank simulation + 177 and available from https://doi.org/10.5281/zenodo.1487761. sameAs: https://doi.org/10.5281/zenodo.1487761 datePublished: '2018-11-14' license: @@ -155,7 +161,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1487761 identifier: 10.5281/zenodo.1487761 url: https://doi.org/10.5281/zenodo.1487761 - name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS with the lipid17 force field, only counterions, and CaCl2 concentrations + name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS + with the lipid17 force field, only counterions, and CaCl2 concentrations publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/8af/d66/8afd667c5df78a5d523d6e7314d01d9dd8fff686/ffcc827026f7f9475602811c00a961261b4ec494/README.yaml b/Simulations/8af/d66/8afd667c5df78a5d523d6e7314d01d9dd8fff686/ffcc827026f7f9475602811c00a961261b4ec494/README.yaml index fa14d0c993..a3a082a542 100644 --- a/Simulations/8af/d66/8afd667c5df78a5d523d6e7314d01d9dd8fff686/ffcc827026f7f9475602811c00a961261b4ec494/README.yaml +++ b/Simulations/8af/d66/8afd667c5df78a5d523d6e7314d01d9dd8fff686/ffcc827026f7f9475602811c00a961261b4ec494/README.yaml @@ -48,9 +48,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 705 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (71:29) bilayer at 298.15 K (MacRog, GROMACS 2021, 1001 ns) [NMRlipids simulation 705] + name: Molecular dynamics trajectory of a POPC/CHOL (71:29) bilayer at 298.15 K (MacRog, + GROMACS 2021, 1001 ns) [NMRlipids simulation 705] alternateName: MacRog_POPC_CHOL29_L - description: Molecular dynamics trajectory of a lipid bilayer of 1024 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 71 mol%) and 416 CHOL (cholesterol, 29 mol%) at 298.15 K. Simulated with MacRog in GROMACS 2021 for 1001 ns (384000 atoms). Deposited as NMRlipids Databank simulation 705 and available from https://doi.org/10.5281/zenodo.7061800. + description: Molecular dynamics trajectory of a lipid bilayer of 1024 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 71 mol%) and 416 CHOL (cholesterol, 29 mol%) at 298.15 K. Simulated with MacRog + in GROMACS 2021 for 1001 ns (384000 atoms). Deposited as NMRlipids Databank simulation + 705 and available from https://doi.org/10.5281/zenodo.7061800. sameAs: https://doi.org/10.5281/zenodo.7061800 datePublished: '2022-09-08' license: diff --git a/Simulations/8b0/60c/8b060ca3d6f6518f9ddddfabf34ce5bed4ddd81c/f8c45a12987ef6c1ad4dfe1d4b5ea865b8afe0b0/README.yaml b/Simulations/8b0/60c/8b060ca3d6f6518f9ddddfabf34ce5bed4ddd81c/f8c45a12987ef6c1ad4dfe1d4b5ea865b8afe0b0/README.yaml index 089996900a..cf5ffc3ee3 100644 --- a/Simulations/8b0/60c/8b060ca3d6f6518f9ddddfabf34ce5bed4ddd81c/f8c45a12987ef6c1ad4dfe1d4b5ea865b8afe0b0/README.yaml +++ b/Simulations/8b0/60c/8b060ca3d6f6518f9ddddfabf34ce5bed4ddd81c/f8c45a12987ef6c1ad4dfe1d4b5ea865b8afe0b0/README.yaml @@ -54,9 +54,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/9 ID: 543 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (53:47) bilayer at 298.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 543] + name: Molecular dynamics trajectory of a POPC/CHOL (53:47) bilayer at 298.15 K (CHARMM36, + GROMACS, 1001 ns) [NMRlipids simulation 543] alternateName: 1024POPC_896CHOL_96000SOL_298K - description: Molecular dynamics trajectory of a lipid bilayer of 1024 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 53 mol%) and 896 CHOL (cholesterol, 47 mol%) at 298.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (491520 atoms). Deposited as NMRlipids Databank simulation 543 and available from https://doi.org/10.5281/zenodo.5767451. + description: Molecular dynamics trajectory of a lipid bilayer of 1024 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 53 mol%) and 896 CHOL (cholesterol, 47 mol%) at 298.15 K. Simulated with CHARMM36 + in GROMACS for 1001 ns (491520 atoms). Deposited as NMRlipids Databank simulation + 543 and available from https://doi.org/10.5281/zenodo.5767451. sameAs: https://doi.org/10.5281/zenodo.5767451 datePublished: '2021-12-08' license: diff --git a/Simulations/8b0/f90/8b0f9005d3e4fe16553e48aebae19950d5e35cae/02e7f972c04717b2e92abd4094778b96b77a7055/README.yaml b/Simulations/8b0/f90/8b0f9005d3e4fe16553e48aebae19950d5e35cae/02e7f972c04717b2e92abd4094778b96b77a7055/README.yaml index c298ce34ef..3c0ad45ee6 100644 --- a/Simulations/8b0/f90/8b0f9005d3e4fe16553e48aebae19950d5e35cae/02e7f972c04717b2e92abd4094778b96b77a7055/README.yaml +++ b/Simulations/8b0/f90/8b0f9005d3e4fe16553e48aebae19950d5e35cae/02e7f972c04717b2e92abd4094778b96b77a7055/README.yaml @@ -49,9 +49,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/5 ID: 706 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (80:20) bilayer at 298.15 K (MacRog, GROMACS 2021, 1001 ns) [NMRlipids simulation 706] + name: Molecular dynamics trajectory of a POPC/CHOL (80:20) bilayer at 298.15 K (MacRog, + GROMACS 2021, 1001 ns) [NMRlipids simulation 706] alternateName: MacRog_POPC_CHOL20_M - description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 80 mol%) and 64 CHOL (cholesterol, 20 mol%) at 298.15 K. Simulated with MacRog in GROMACS 2021 for 1001 ns (87040 atoms). Deposited as NMRlipids Databank simulation 706 and available from https://doi.org/10.5281/zenodo.7061800. + description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 80 mol%) and 64 CHOL (cholesterol, 20 mol%) at 298.15 K. Simulated with MacRog + in GROMACS 2021 for 1001 ns (87040 atoms). Deposited as NMRlipids Databank simulation + 706 and available from https://doi.org/10.5281/zenodo.7061800. sameAs: https://doi.org/10.5281/zenodo.7061800 datePublished: '2022-09-08' license: diff --git a/Simulations/8b4/def/8b4defac09883665a8c2e32302d5080664fc77aa/f0b754bfeb545d99e3d319216c6894adbf27fee2/README.yaml b/Simulations/8b4/def/8b4defac09883665a8c2e32302d5080664fc77aa/f0b754bfeb545d99e3d319216c6894adbf27fee2/README.yaml index 38751bb8fc..d4f598a519 100644 --- a/Simulations/8b4/def/8b4defac09883665a8c2e32302d5080664fc77aa/f0b754bfeb545d99e3d319216c6894adbf27fee2/README.yaml +++ b/Simulations/8b4/def/8b4defac09883665a8c2e32302d5080664fc77aa/f0b754bfeb545d99e3d319216c6894adbf27fee2/README.yaml @@ -43,9 +43,14 @@ SOFTWARE: gromacs DIR_WRK: /usr/home/bort/Databank ID: 199 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC bilayer at 325 K (CHARMM36 (center of mass removed independently for upper leaflet, lower leaflet and water+ions), GROMACS 5.0.4, 500 ns) [NMRlipids simulation 199] + name: Molecular dynamics trajectory of a DPPC bilayer at 325 K (CHARMM36 (center + of mass removed independently for upper leaflet, lower leaflet and water+ions), + GROMACS 5.0.4, 500 ns) [NMRlipids simulation 199] alternateName: 72DPPC_2188SOL_325K_rmcomm_leaflets - description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) at 325 K. Simulated with CHARMM36 (center of mass removed independently for upper leaflet, lower leaflet and water+ions) in GROMACS 5.0.4 for 500 ns (15924 atoms). Deposited as NMRlipids Databank simulation 199 and available from https://doi.org/10.5281/zenodo.1009607. + description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) + at 325 K. Simulated with CHARMM36 (center of mass removed independently for upper + leaflet, lower leaflet and water+ions) in GROMACS 5.0.4 for 500 ns (15924 atoms). + Deposited as NMRlipids Databank simulation 199 and available from https://doi.org/10.5281/zenodo.1009607. sameAs: https://doi.org/10.5281/zenodo.1009607 datePublished: '2017-10-12' license: @@ -98,7 +103,8 @@ bioschema_properties: inDefinedTermSet: http://edamontology.org url: http://edamontology.org/operation_2476 - Molecular dynamics simulation (gromacs 5.0.4) - - CHARMM36 (center of mass removed independently for upper leaflet, lower leaflet and water+ions) force field + - CHARMM36 (center of mass removed independently for upper leaflet, lower leaflet + and water+ions) force field variableMeasured: - '@type': PropertyValue name: area per lipid @@ -140,7 +146,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1009607 identifier: 10.5281/zenodo.1009607 url: https://doi.org/10.5281/zenodo.1009607 - name: Set Simulations Small Pure Bilayers (72 Lipids) Using Charmm36 Ff In Gromacs (Dppc, Popc) + name: Set Simulations Small Pure Bilayers (72 Lipids) Using Charmm36 Ff In Gromacs + (Dppc, Popc) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/8bd/67c/8bd67cee9e378f25ad0826c4da436e44d72038be/6a3d11e69a7d3d3bac227a6ba9b74b05548c2fe6/README.yaml b/Simulations/8bd/67c/8bd67cee9e378f25ad0826c4da436e44d72038be/6a3d11e69a7d3d3bac227a6ba9b74b05548c2fe6/README.yaml index b1951083bc..d13cec7676 100644 --- a/Simulations/8bd/67c/8bd67cee9e378f25ad0826c4da436e44d72038be/6a3d11e69a7d3d3bac227a6ba9b74b05548c2fe6/README.yaml +++ b/Simulations/8bd/67c/8bd67cee9e378f25ad0826c4da436e44d72038be/6a3d11e69a7d3d3bac227a6ba9b74b05548c2fe6/README.yaml @@ -43,9 +43,13 @@ TRJ: TEMPERATURE: 300.0 ID: 149 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPE (50:50) bilayer at 300 K (MacRog, GROMACS, 500 ns) [NMRlipids simulation 149] + name: Molecular dynamics trajectory of a POPC/POPE (50:50) bilayer at 300 K (MacRog, + GROMACS, 500 ns) [NMRlipids simulation 149] alternateName: POPC:POPE(1:1)_T300K - description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 50 mol%) and 64 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 50 mol%) at 300 K. Simulated with MacRog in GROMACS for 500 ns (31936 atoms). Deposited as NMRlipids Databank simulation 149 and available from https://doi.org/10.5281/zenodo.3725637. + description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 50 mol%) and 64 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 50 + mol%) at 300 K. Simulated with MacRog in GROMACS for 500 ns (31936 atoms). Deposited + as NMRlipids Databank simulation 149 and available from https://doi.org/10.5281/zenodo.3725637. sameAs: https://doi.org/10.5281/zenodo.3725637 datePublished: '2020-03-26' license: diff --git a/Simulations/8c0/bf9/8c0bf9095dfae25b09fef6633bd919ce08743f88/b6bf70bcc38d00a7bd8d4c02ef2d8f73d3806f46/README.yaml b/Simulations/8c0/bf9/8c0bf9095dfae25b09fef6633bd919ce08743f88/b6bf70bcc38d00a7bd8d4c02ef2d8f73d3806f46/README.yaml index 99303e4e40..1df4a79ad0 100644 --- a/Simulations/8c0/bf9/8c0bf9095dfae25b09fef6633bd919ce08743f88/b6bf70bcc38d00a7bd8d4c02ef2d8f73d3806f46/README.yaml +++ b/Simulations/8c0/bf9/8c0bf9095dfae25b09fef6633bd919ce08743f88/b6bf70bcc38d00a7bd8d4c02ef2d8f73d3806f46/README.yaml @@ -41,9 +41,12 @@ EXPERIMENT: SM18: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a SM18 bilayer at 328.15 K (CHARMM36, GROMACS 2020.4 and 2021.4, 150 ns) [NMRlipids simulation 763] + name: Molecular dynamics trajectory of a SM18 bilayer at 328.15 K (CHARMM36, GROMACS + 2020.4 and 2021.4, 150 ns) [NMRlipids simulation 763] alternateName: SSM bilayer in water, 328K - description: Molecular dynamics trajectory of a lipid bilayer of 128 SM18 (N-stearoyl-D-erythro-sphingosylphosphorylcholine) at 328.15 K. Simulated with CHARMM36 in GROMACS 2020.4 and 2021.4 for 150 ns (32384 atoms). Deposited as NMRlipids Databank simulation 763 and available from https://doi.org/10.5281/zenodo.8333993. + description: Molecular dynamics trajectory of a lipid bilayer of 128 SM18 (N-stearoyl-D-erythro-sphingosylphosphorylcholine) + at 328.15 K. Simulated with CHARMM36 in GROMACS 2020.4 and 2021.4 for 150 ns (32384 + atoms). Deposited as NMRlipids Databank simulation 763 and available from https://doi.org/10.5281/zenodo.8333993. sameAs: https://doi.org/10.5281/zenodo.8333993 datePublished: '2023-09-11' license: diff --git a/Simulations/8ca/000/8ca00036c7b2651777029af5432ab0dbdd369e55/ddda204aa8857c2b9193e9eed192359ede29420f/README.yaml b/Simulations/8ca/000/8ca00036c7b2651777029af5432ab0dbdd369e55/ddda204aa8857c2b9193e9eed192359ede29420f/README.yaml index 58a173816e..e41c369df1 100644 --- a/Simulations/8ca/000/8ca00036c7b2651777029af5432ab0dbdd369e55/ddda204aa8857c2b9193e9eed192359ede29420f/README.yaml +++ b/Simulations/8ca/000/8ca00036c7b2651777029af5432ab0dbdd369e55/ddda204aa8857c2b9193e9eed192359ede29420f/README.yaml @@ -61,9 +61,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 111 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/SOD/CLA/POPS (37:31:24:7) bilayer at 298 K (ECC-lipids, GROMACS 2018.0, 975 ns) [NMRlipids simulation 111] + name: Molecular dynamics trajectory of a POPC/SOD/CLA/POPS (37:31:24:7) bilayer + at 298 K (ECC-lipids, GROMACS 2018.0, 975 ns) [NMRlipids simulation 111] alternateName: 12POPS_60POPC_3483SOL_51SOD_39CLA_298K - description: Molecular dynamics trajectory of a lipid bilayer of 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 37 mol%), 51 SOD (31 mol%), 39 CLA (24 mol%) and 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 7 mol%) at 298 K. Simulated with ECC-lipids in GROMACS 2018.0 for 975 ns (20103 atoms). Deposited as NMRlipids Databank simulation 111 and available from https://doi.org/10.5281/zenodo.3332778. + description: Molecular dynamics trajectory of a lipid bilayer of 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 37 mol%), 51 SOD (31 mol%), 39 CLA (24 mol%) and 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, + 7 mol%) at 298 K. Simulated with ECC-lipids in GROMACS 2018.0 for 975 ns (20103 + atoms). Deposited as NMRlipids Databank simulation 111 and available from https://doi.org/10.5281/zenodo.3332778. sameAs: https://doi.org/10.5281/zenodo.3332778 datePublished: '2018-11-14' license: @@ -155,7 +159,9 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3332778 identifier: 10.5281/zenodo.3332778 url: https://doi.org/10.5281/zenodo.3332778 - name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS (5:1) with ECC-lipids force field, and Na+ (K+) counterions at various additional concentrations of NaCl and KCl + name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS + (5:1) with ECC-lipids force field, and Na+ (K+) counterions at various additional + concentrations of NaCl and KCl publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/8cb/989/8cb989e1813b93d1144d731ffbbc04a5cfcfb6a6/2db4e1d512355edd21cedbc0d28a45659dd6faa9/README.yaml b/Simulations/8cb/989/8cb989e1813b93d1144d731ffbbc04a5cfcfb6a6/2db4e1d512355edd21cedbc0d28a45659dd6faa9/README.yaml index fb805cc24d..1737cac26e 100644 --- a/Simulations/8cb/989/8cb989e1813b93d1144d731ffbbc04a5cfcfb6a6/2db4e1d512355edd21cedbc0d28a45659dd6faa9/README.yaml +++ b/Simulations/8cb/989/8cb989e1813b93d1144d731ffbbc04a5cfcfb6a6/2db4e1d512355edd21cedbc0d28a45659dd6faa9/README.yaml @@ -44,9 +44,13 @@ TRJ: DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 82 bioschema_properties: - name: Molecular dynamics trajectory of a CHOL/POPC (50:50) bilayer at 298 K (slipids, GROMACS 4.6.3, 100 ns) [NMRlipids simulation 82] + name: Molecular dynamics trajectory of a CHOL/POPC (50:50) bilayer at 298 K (slipids, + GROMACS 4.6.3, 100 ns) [NMRlipids simulation 82] alternateName: POPC:CHOL(1:1)_T298K - description: Molecular dynamics trajectory of a lipid bilayer of 256 CHOL (cholesterol, 50 mol%) and 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 50 mol%) at 298 K. Simulated with slipids in GROMACS 4.6.3 for 100 ns (114250 atoms). Deposited as NMRlipids Databank simulation 82 and available from https://doi.org/10.5281/zenodo.159434. + description: Molecular dynamics trajectory of a lipid bilayer of 256 CHOL (cholesterol, + 50 mol%) and 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 50 mol%) + at 298 K. Simulated with slipids in GROMACS 4.6.3 for 100 ns (114250 atoms). Deposited + as NMRlipids Databank simulation 82 and available from https://doi.org/10.5281/zenodo.159434. sameAs: https://doi.org/10.5281/zenodo.159434 datePublished: '2016-10-05' license: @@ -138,7 +142,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.159434 identifier: 10.5281/zenodo.159434 url: https://doi.org/10.5281/zenodo.159434 - name: 'Md Simulation Trajectory Of A Lipid Bilayer: 50/50 Mol% Popc/Cholesterol . Slipids, Gromacs 4.6.3. 2016.' + name: 'Md Simulation Trajectory Of A Lipid Bilayer: 50/50 Mol% Popc/Cholesterol + . Slipids, Gromacs 4.6.3. 2016.' publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/8ce/23b/8ce23bb33af41c05a6f9e78ee540b0f0b3d80b61/8e30fa47b8446f2eb523b55d501f6c6ea6e39675/README.yaml b/Simulations/8ce/23b/8ce23bb33af41c05a6f9e78ee540b0f0b3d80b61/8e30fa47b8446f2eb523b55d501f6c6ea6e39675/README.yaml index ccf786bc28..522776fb7f 100644 --- a/Simulations/8ce/23b/8ce23bb33af41c05a6f9e78ee540b0f0b3d80b61/8e30fa47b8446f2eb523b55d501f6c6ea6e39675/README.yaml +++ b/Simulations/8ce/23b/8ce23bb33af41c05a6f9e78ee540b0f0b3d80b61/8e30fa47b8446f2eb523b55d501f6c6ea6e39675/README.yaml @@ -40,9 +40,12 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 608 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC bilayer at 348 K (CHARMM36, GROMACS 2016.4, 49 ns) [NMRlipids simulation 608] + name: Molecular dynamics trajectory of a DPPC bilayer at 348 K (CHARMM36, GROMACS + 2016.4, 49 ns) [NMRlipids simulation 608] alternateName: 212DPPC_29826SOL_348K - description: Molecular dynamics trajectory of a lipid bilayer of 212 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) at 348 K. Simulated with CHARMM36 in GROMACS 2016.4 for 49 ns (117038 atoms). Deposited as NMRlipids Databank simulation 608 and available from https://doi.org/10.5281/zenodo.3950029. + description: Molecular dynamics trajectory of a lipid bilayer of 212 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) + at 348 K. Simulated with CHARMM36 in GROMACS 2016.4 for 49 ns (117038 atoms). + Deposited as NMRlipids Databank simulation 608 and available from https://doi.org/10.5281/zenodo.3950029. sameAs: https://doi.org/10.5281/zenodo.3950029 datePublished: '2020-07-20' license: @@ -142,7 +145,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3950029 identifier: 10.5281/zenodo.3950029 url: https://doi.org/10.5281/zenodo.3950029 - name: 212 DPPC Molecules bilayer in pure Water, simulated at temperatures ranging from 288K to 358K + name: 212 DPPC Molecules bilayer in pure Water, simulated at temperatures ranging + from 288K to 358K publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/8d8/5c6/8d85c662a53e14e285a3bcfb75c55f3fef35be4b/343a5f2b56bf580ab0e4fb5d444c2c947c825dd3/README.yaml b/Simulations/8d8/5c6/8d85c662a53e14e285a3bcfb75c55f3fef35be4b/343a5f2b56bf580ab0e4fb5d444c2c947c825dd3/README.yaml index 4ba3d01fd4..b26300ad89 100644 --- a/Simulations/8d8/5c6/8d85c662a53e14e285a3bcfb75c55f3fef35be4b/343a5f2b56bf580ab0e4fb5d444c2c947c825dd3/README.yaml +++ b/Simulations/8d8/5c6/8d85c662a53e14e285a3bcfb75c55f3fef35be4b/343a5f2b56bf580ab0e4fb5d444c2c947c825dd3/README.yaml @@ -54,9 +54,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 10 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (49:34:17) bilayer at 298 K (Berger delivered by Peter Tieleman, GROMACS 4.5, 58 ns) [NMRlipids simulation 10] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (49:34:17) bilayer at 298 + K (Berger delivered by Peter Tieleman, GROMACS 4.5, 58 ns) [NMRlipids simulation + 10] alternateName: 128POPC_44CAL_88CLA_7157SOL_298K_Berger - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 49 mol%), 88 CLA (34 mol%) and 44 CAL (17 mol%) at 298 K. Simulated with Berger delivered by Peter Tieleman in GROMACS 4.5 for 58 ns (28259 atoms). Deposited as NMRlipids Databank simulation 10 and available from https://doi.org/10.5281/zenodo.32173. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 49 mol%), 88 CLA (34 mol%) and 44 CAL (17 mol%) at 298 K. Simulated with Berger + delivered by Peter Tieleman in GROMACS 4.5 for 58 ns (28259 atoms). Deposited + as NMRlipids Databank simulation 10 and available from https://doi.org/10.5281/zenodo.32173. sameAs: https://doi.org/10.5281/zenodo.32173 datePublished: '2015-10-16' license: @@ -145,7 +150,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.32173 identifier: 10.5281/zenodo.32173 url: https://doi.org/10.5281/zenodo.32173 - name: Md Simulation Trajectory And Related Files For Popc Bilayer With 340Mm Cacl_2 (Berger Model Delivered By Tieleman, Ffgmx Ions, Gromacs 4.5) + name: Md Simulation Trajectory And Related Files For Popc Bilayer With 340Mm Cacl_2 + (Berger Model Delivered By Tieleman, Ffgmx Ions, Gromacs 4.5) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/8da/bbf/8dabbfbd36d2a4c9a77b77f9c7f82545a38f2e12/91ff979f3bf6d468835a097c3d329cb9b08627db/README.yaml b/Simulations/8da/bbf/8dabbfbd36d2a4c9a77b77f9c7f82545a38f2e12/91ff979f3bf6d468835a097c3d329cb9b08627db/README.yaml index 7754a92a23..71b27e62ea 100644 --- a/Simulations/8da/bbf/8dabbfbd36d2a4c9a77b77f9c7f82545a38f2e12/91ff979f3bf6d468835a097c3d329cb9b08627db/README.yaml +++ b/Simulations/8da/bbf/8dabbfbd36d2a4c9a77b77f9c7f82545a38f2e12/91ff979f3bf6d468835a097c3d329cb9b08627db/README.yaml @@ -43,9 +43,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 577 bioschema_properties: - name: Molecular dynamics trajectory of a DOPC bilayer at 333.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 577] + name: Molecular dynamics trajectory of a DOPC bilayer at 333.15 K (CHARMM36, GROMACS, + 1001 ns) [NMRlipids simulation 577] alternateName: 64DOPC_3200SOL_333K - description: Molecular dynamics trajectory of a lipid bilayer of 64 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (18432 atoms). Deposited as NMRlipids Databank simulation 577 and available from https://doi.org/10.5281/zenodo.6943413. + description: Molecular dynamics trajectory of a lipid bilayer of 64 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) + at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (18432 atoms). Deposited + as NMRlipids Databank simulation 577 and available from https://doi.org/10.5281/zenodo.6943413. sameAs: https://doi.org/10.5281/zenodo.6943413 datePublished: '2022-07-30' license: @@ -133,7 +136,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.6943413 identifier: 10.5281/zenodo.6943413 url: https://doi.org/10.5281/zenodo.6943413 - name: Simulations of different single-component bilayers, three different system sizes + name: Simulations of different single-component bilayers, three different system + sizes publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/8e6/368/8e63681c396736ae1c0cba23100edfe9ae506bbb/92f8bf2f1cdcc3b9c791a2b78cbef9a6b1916c15/README.yaml b/Simulations/8e6/368/8e63681c396736ae1c0cba23100edfe9ae506bbb/92f8bf2f1cdcc3b9c791a2b78cbef9a6b1916c15/README.yaml index b60a5e4aa2..da78338d82 100644 --- a/Simulations/8e6/368/8e63681c396736ae1c0cba23100edfe9ae506bbb/92f8bf2f1cdcc3b9c791a2b78cbef9a6b1916c15/README.yaml +++ b/Simulations/8e6/368/8e63681c396736ae1c0cba23100edfe9ae506bbb/92f8bf2f1cdcc3b9c791a2b78cbef9a6b1916c15/README.yaml @@ -52,9 +52,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/9 ID: 707 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (53:47) bilayer at 298.15 K (Lipid17, GROMACS 2021, 1001 ns) [NMRlipids simulation 707] + name: Molecular dynamics trajectory of a POPC/CHOL (53:47) bilayer at 298.15 K (Lipid17, + GROMACS 2021, 1001 ns) [NMRlipids simulation 707] alternateName: Lipid17_POPC_CHOL47_S - description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 53 mol%) and 56 CHOL (cholesterol, 47 mol%) at 298.15 K. Simulated with Lipid17 in GROMACS 2021 for 1001 ns (30720 atoms). Deposited as NMRlipids Databank simulation 707 and available from https://doi.org/10.5281/zenodo.6992065. + description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 53 mol%) and 56 CHOL (cholesterol, 47 mol%) at 298.15 K. Simulated with Lipid17 + in GROMACS 2021 for 1001 ns (30720 atoms). Deposited as NMRlipids Databank simulation + 707 and available from https://doi.org/10.5281/zenodo.6992065. sameAs: https://doi.org/10.5281/zenodo.6992065 datePublished: '2022-08-15' license: diff --git a/Simulations/8e7/445/8e74451d42d164085406e42824c21afda1a3f433/1005584fb9c9b92a58c3818603e351aceabb53d4/README.yaml b/Simulations/8e7/445/8e74451d42d164085406e42824c21afda1a3f433/1005584fb9c9b92a58c3818603e351aceabb53d4/README.yaml index cb90745a02..c18090927e 100644 --- a/Simulations/8e7/445/8e74451d42d164085406e42824c21afda1a3f433/1005584fb9c9b92a58c3818603e351aceabb53d4/README.yaml +++ b/Simulations/8e7/445/8e74451d42d164085406e42824c21afda1a3f433/1005584fb9c9b92a58c3818603e351aceabb53d4/README.yaml @@ -44,9 +44,12 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/1 ID: 708 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 298.15 K (Slipids, GROMACS 2021, 1001 ns) [NMRlipids simulation 708] + name: Molecular dynamics trajectory of a POPC bilayer at 298.15 K (Slipids, GROMACS + 2021, 1001 ns) [NMRlipids simulation 708] alternateName: Slipids_POPC_M - description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 298.15 K. Simulated with Slipids in GROMACS 2021 for 1001 ns (72704 atoms). Deposited as NMRlipids Databank simulation 708 and available from https://doi.org/10.5281/zenodo.7022749. + description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 298.15 K. Simulated with Slipids in GROMACS 2021 for 1001 ns (72704 atoms). + Deposited as NMRlipids Databank simulation 708 and available from https://doi.org/10.5281/zenodo.7022749. sameAs: https://doi.org/10.5281/zenodo.7022749 datePublished: '2022-08-23' license: diff --git a/Simulations/8ea/f33/8eaf33ff270a3ffb78a6a2cb66dcf0e39a7b6eeb/8eaf33ff270a3ffb78a6a2cb66dcf0e39a7b6eeb/README.yaml b/Simulations/8ea/f33/8eaf33ff270a3ffb78a6a2cb66dcf0e39a7b6eeb/8eaf33ff270a3ffb78a6a2cb66dcf0e39a7b6eeb/README.yaml index a532088f02..7bb97e4418 100644 --- a/Simulations/8ea/f33/8eaf33ff270a3ffb78a6a2cb66dcf0e39a7b6eeb/8eaf33ff270a3ffb78a6a2cb66dcf0e39a7b6eeb/README.yaml +++ b/Simulations/8ea/f33/8eaf33ff270a3ffb78a6a2cb66dcf0e39a7b6eeb/8eaf33ff270a3ffb78a6a2cb66dcf0e39a7b6eeb/README.yaml @@ -45,9 +45,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 739 bioschema_properties: - name: Molecular dynamics trajectory of a CLA/DOPC/CAL (40:40:20) bilayer at 303 K (AMOEBA, OPENMM v7.5.1, 218 ns) [NMRlipids simulation 739] + name: Molecular dynamics trajectory of a CLA/DOPC/CAL (40:40:20) bilayer at 303 + K (AMOEBA, OPENMM v7.5.1, 218 ns) [NMRlipids simulation 739] alternateName: DOPC_1000mM_CaCl2_at_303K_with_AMOEBA - description: Molecular dynamics trajectory of a lipid bilayer of 72 CLA (40 mol%), 72 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, 40 mol%) and 36 CAL (20 mol%) at 303 K. Simulated with AMOEBA in OPENMM v7.5.1 for 218 ns (18684 atoms). Deposited as NMRlipids Databank simulation 739 and available from https://doi.org/10.5281/zenodo.7604810. + description: Molecular dynamics trajectory of a lipid bilayer of 72 CLA (40 mol%), + 72 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, 40 mol%) and 36 CAL (20 mol%) + at 303 K. Simulated with AMOEBA in OPENMM v7.5.1 for 218 ns (18684 atoms). Deposited + as NMRlipids Databank simulation 739 and available from https://doi.org/10.5281/zenodo.7604810. sameAs: https://doi.org/10.5281/zenodo.7604810 datePublished: '2022-12-11' license: @@ -135,7 +139,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.7604810 identifier: 10.5281/zenodo.7604810 url: https://doi.org/10.5281/zenodo.7604810 - name: MD Simulation data for a pure DOPC bilayer (1000 mM CaCl2) with AMOEBA force field + OpenMM + name: MD Simulation data for a pure DOPC bilayer (1000 mM CaCl2) with AMOEBA force + field + OpenMM publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/8f1/5d1/8f15d1f68952e3d1b79be9066cbeb3c562d8c83d/480df0d527104e587dfb197ed8dff90b3872d75d/README.yaml b/Simulations/8f1/5d1/8f15d1f68952e3d1b79be9066cbeb3c562d8c83d/480df0d527104e587dfb197ed8dff90b3872d75d/README.yaml index f5bf631d06..8e9c258e2e 100644 --- a/Simulations/8f1/5d1/8f15d1f68952e3d1b79be9066cbeb3c562d8c83d/480df0d527104e587dfb197ed8dff90b3872d75d/README.yaml +++ b/Simulations/8f1/5d1/8f15d1f68952e3d1b79be9066cbeb3c562d8c83d/480df0d527104e587dfb197ed8dff90b3872d75d/README.yaml @@ -54,9 +54,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 401 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPS/SOD (67:17:17) bilayer at 298 K (ECC-lipids, SPC water model, ECC-ions, GROMACS 2018.0, 982 ns) [NMRlipids simulation 401] + name: Molecular dynamics trajectory of a POPC/POPS/SOD (67:17:17) bilayer at 298 + K (ECC-lipids, SPC water model, ECC-ions, GROMACS 2018.0, 982 ns) [NMRlipids simulation + 401] alternateName: 12POPS_48POPC_3600SOL_12SOD_298K_ECC-lipid - description: Molecular dynamics trajectory of a lipid bilayer of 48 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 67 mol%), 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 17 mol%) and 12 SOD (17 mol%) at 298 K. Simulated with ECC-lipids, SPC water model, ECC-ions in GROMACS 2018.0 for 982 ns (18768 atoms). Deposited as NMRlipids Databank simulation 401 and available from https://doi.org/10.5281/zenodo.1488094. + description: Molecular dynamics trajectory of a lipid bilayer of 48 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 67 mol%), 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 17 mol%) + and 12 SOD (17 mol%) at 298 K. Simulated with ECC-lipids, SPC water model, ECC-ions + in GROMACS 2018.0 for 982 ns (18768 atoms). Deposited as NMRlipids Databank simulation + 401 and available from https://doi.org/10.5281/zenodo.1488094. sameAs: https://doi.org/10.5281/zenodo.1488094 datePublished: '2018-11-14' license: @@ -147,7 +153,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1488094 identifier: 10.5281/zenodo.1488094 url: https://doi.org/10.5281/zenodo.1488094 - name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS (various mixtures) with ECC-lipids force field, and Na+ (K+) counterions + name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS + (various mixtures) with ECC-lipids force field, and Na+ (K+) counterions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/8f4/59c/8f459c415f10c8871360ca97ce3d29b4ba956142/91b5cc9714f20ded49639d9dcbaeaf84566bf6d0/README.yaml b/Simulations/8f4/59c/8f459c415f10c8871360ca97ce3d29b4ba956142/91b5cc9714f20ded49639d9dcbaeaf84566bf6d0/README.yaml index 6bde0fbacd..d6f55fbc94 100644 --- a/Simulations/8f4/59c/8f459c415f10c8871360ca97ce3d29b4ba956142/91b5cc9714f20ded49639d9dcbaeaf84566bf6d0/README.yaml +++ b/Simulations/8f4/59c/8f459c415f10c8871360ca97ce3d29b4ba956142/91b5cc9714f20ded49639d9dcbaeaf84566bf6d0/README.yaml @@ -57,9 +57,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 11 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD/CER (72:11:11:7) bilayer at 310 K (CHARMM36, GROMACS 2016.2, 3497 ns) [NMRlipids simulation 11] + name: Molecular dynamics trajectory of a POPC/CLA/SOD/CER (72:11:11:7) bilayer at + 310 K (CHARMM36, GROMACS 2016.2, 3497 ns) [NMRlipids simulation 11] alternateName: 512POPC_50CER_28100SOL_75SOD_75CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 512 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 72 mol%), 75 CLA (11 mol%), 75 SOD (11 mol%) and 50 CER (N-palmitoyl-D-erythro-sphingosine, 7 mol%) at 310 K. Simulated with CHARMM36 in GROMACS 2016.2 for 3497 ns (158308 atoms). Deposited as NMRlipids Databank simulation 11 and available from https://doi.org/10.5281/zenodo.1230390. + description: Molecular dynamics trajectory of a lipid bilayer of 512 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 72 mol%), 75 CLA (11 mol%), 75 SOD (11 mol%) and 50 CER (N-palmitoyl-D-erythro-sphingosine, + 7 mol%) at 310 K. Simulated with CHARMM36 in GROMACS 2016.2 for 3497 ns (158308 + atoms). Deposited as NMRlipids Databank simulation 11 and available from https://doi.org/10.5281/zenodo.1230390. sameAs: https://doi.org/10.5281/zenodo.1230390 datePublished: '2018-04-26' license: diff --git a/Simulations/8f8/df8/8f8df8010c88fe45e6515d41a85d7555b9f01f1b/d5b534249aea5e638754373da5650eb8309e46b7/README.yaml b/Simulations/8f8/df8/8f8df8010c88fe45e6515d41a85d7555b9f01f1b/d5b534249aea5e638754373da5650eb8309e46b7/README.yaml index 079399d5d2..07bcc028f5 100644 --- a/Simulations/8f8/df8/8f8df8010c88fe45e6515d41a85d7555b9f01f1b/d5b534249aea5e638754373da5650eb8309e46b7/README.yaml +++ b/Simulations/8f8/df8/8f8df8010c88fe45e6515d41a85d7555b9f01f1b/d5b534249aea5e638754373da5650eb8309e46b7/README.yaml @@ -43,9 +43,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 76 bioschema_properties: - name: Molecular dynamics trajectory of a DOPC bilayer at 293.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 76] + name: Molecular dynamics trajectory of a DOPC bilayer at 293.15 K (CHARMM36, GROMACS, + 1001 ns) [NMRlipids simulation 76] alternateName: 1024DOPC_51200SOL_293K - description: Molecular dynamics trajectory of a lipid bilayer of 1024 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) at 293.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (294912 atoms). Deposited as NMRlipids Databank simulation 76 and available from https://doi.org/10.5281/zenodo.6943086. + description: Molecular dynamics trajectory of a lipid bilayer of 1024 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) + at 293.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (294912 atoms). Deposited + as NMRlipids Databank simulation 76 and available from https://doi.org/10.5281/zenodo.6943086. sameAs: https://doi.org/10.5281/zenodo.6943086 datePublished: '2022-07-30' license: diff --git a/Simulations/8f8/e86/8f8e862c263ed75b233d4fb99aa8b8a28ba94af7/575680d4063a7e8ed58846ae71d1c3e3f43fa450/README.yaml b/Simulations/8f8/e86/8f8e862c263ed75b233d4fb99aa8b8a28ba94af7/575680d4063a7e8ed58846ae71d1c3e3f43fa450/README.yaml index 05774f61c7..d4eabb0b68 100644 --- a/Simulations/8f8/e86/8f8e862c263ed75b233d4fb99aa8b8a28ba94af7/575680d4063a7e8ed58846ae71d1c3e3f43fa450/README.yaml +++ b/Simulations/8f8/e86/8f8e862c263ed75b233d4fb99aa8b8a28ba94af7/575680d4063a7e8ed58846ae71d1c3e3f43fa450/README.yaml @@ -51,9 +51,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 75 bioschema_properties: - name: Molecular dynamics trajectory of a DOPE/POPC (50:50) bilayer at 300 K (Berger (modified to add a repulsive potential onto the ethanolamine hydrogens), GROMACS, 300 ns) [NMRlipids simulation 75] + name: Molecular dynamics trajectory of a DOPE/POPC (50:50) bilayer at 300 K (Berger + (modified to add a repulsive potential onto the ethanolamine hydrogens), GROMACS, + 300 ns) [NMRlipids simulation 75] alternateName: 128POPC_128DOPE_11096SOL_300K - description: Molecular dynamics trajectory of a lipid bilayer of 128 DOPE (1,2-dioleoyl-sn-glycero-3-phosphoethanolamine, 50 mol%) and 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 50 mol%) at 300 K. Simulated with Berger (modified to add a repulsive potential onto the ethanolamine hydrogens) in GROMACS for 300 ns (46856 atoms). Deposited as NMRlipids Databank simulation 75 and available from https://doi.org/10.5281/zenodo.1402441. + description: Molecular dynamics trajectory of a lipid bilayer of 128 DOPE (1,2-dioleoyl-sn-glycero-3-phosphoethanolamine, + 50 mol%) and 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 50 mol%) + at 300 K. Simulated with Berger (modified to add a repulsive potential onto the + ethanolamine hydrogens) in GROMACS for 300 ns (46856 atoms). Deposited as NMRlipids + Databank simulation 75 and available from https://doi.org/10.5281/zenodo.1402441. sameAs: https://doi.org/10.5281/zenodo.1402441 datePublished: '2018-08-23' license: @@ -102,7 +108,8 @@ bioschema_properties: inDefinedTermSet: http://edamontology.org url: http://edamontology.org/operation_2476 - Molecular dynamics simulation (gromacs) - - Berger (modified to add a repulsive potential onto the ethanolamine hydrogens) force field + - Berger (modified to add a repulsive potential onto the ethanolamine hydrogens) + force field variableMeasured: - '@type': PropertyValue name: area per lipid diff --git a/Simulations/901/6e5/9016e50fb0f79a2788e434b84354d06ff4427c3e/9016e50fb0f79a2788e434b84354d06ff4427c3e/README.yaml b/Simulations/901/6e5/9016e50fb0f79a2788e434b84354d06ff4427c3e/9016e50fb0f79a2788e434b84354d06ff4427c3e/README.yaml index f5afd4a11a..b832b8d995 100644 --- a/Simulations/901/6e5/9016e50fb0f79a2788e434b84354d06ff4427c3e/9016e50fb0f79a2788e434b84354d06ff4427c3e/README.yaml +++ b/Simulations/901/6e5/9016e50fb0f79a2788e434b84354d06ff4427c3e/9016e50fb0f79a2788e434b84354d06ff4427c3e/README.yaml @@ -37,9 +37,12 @@ EXPERIMENT: FORMFACTOR: - 10.1016/j.chemphyslip.2020.104892/1 bioschema_properties: - name: Molecular dynamics trajectory of a PDPC bilayer at 303.15 K (CHARMM36m, NAMD 3, 500 ns) [NMRlipids simulation 902] + name: Molecular dynamics trajectory of a PDPC bilayer at 303.15 K (CHARMM36m, NAMD + 3, 500 ns) [NMRlipids simulation 902] alternateName: PDPC - description: Molecular dynamics trajectory of a lipid bilayer of 200 PDPC (1-palmitoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine) at 303.15 K. Simulated with CHARMM36m in NAMD 3 for 500 ns (54200 atoms). Deposited as NMRlipids Databank simulation 902 and available from https://doi.org/10.5281/zenodo.18471696. + description: Molecular dynamics trajectory of a lipid bilayer of 200 PDPC (1-palmitoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine) + at 303.15 K. Simulated with CHARMM36m in NAMD 3 for 500 ns (54200 atoms). Deposited + as NMRlipids Databank simulation 902 and available from https://doi.org/10.5281/zenodo.18471696. sameAs: https://doi.org/10.5281/zenodo.18471696 datePublished: '2026-02-03' license: @@ -130,7 +133,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.18471696 identifier: 10.5281/zenodo.18471696 url: https://doi.org/10.5281/zenodo.18471696 - name: 1-palmitoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine (PDPC) lipid bilayer , 303K, CHARMM36m-WYF forcefield, NAMD 3.0.2, 2* 500 ns + name: 1-palmitoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine (PDPC) lipid bilayer + , 303K, CHARMM36m-WYF forcefield, NAMD 3.0.2, 2* 500 ns publisher: Zenodo _source: api: datacite diff --git a/Simulations/902/649/90264920ee5640b7c18082ff86a7fcc0b9bd75ea/b6e03a197721f25e989d3452166ec5f88ca0aae4/README.yaml b/Simulations/902/649/90264920ee5640b7c18082ff86a7fcc0b9bd75ea/b6e03a197721f25e989d3452166ec5f88ca0aae4/README.yaml index b70e6d73c5..dc4b01e6a5 100644 --- a/Simulations/902/649/90264920ee5640b7c18082ff86a7fcc0b9bd75ea/b6e03a197721f25e989d3452166ec5f88ca0aae4/README.yaml +++ b/Simulations/902/649/90264920ee5640b7c18082ff86a7fcc0b9bd75ea/b6e03a197721f25e989d3452166ec5f88ca0aae4/README.yaml @@ -54,9 +54,15 @@ EXPERIMENT: ID: 32 AUTHORS_CONTACT: Javanainen, Matti bioschema_properties: - name: Molecular dynamics trajectory of a CLA/CAL/POPC/POPG/SOD (43:21:12:12:12) bilayer at 298 K (Slipids, GROMACS, 1000 ns) [NMRlipids simulation 32] + name: Molecular dynamics trajectory of a CLA/CAL/POPC/POPG/SOD (43:21:12:12:12) + bilayer at 298 K (Slipids, GROMACS, 1000 ns) [NMRlipids simulation 32] alternateName: POPC_POPG_1:1_1000mMCaCL2 - description: Molecular dynamics trajectory of a lipid bilayer of 460 CLA (43 mol%), 230 CAL (21 mol%), 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 12 mol%), 128 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 12 mol%) and 128 SOD (12 mol%) at 298 K. Simulated with Slipids in GROMACS for 1000 ns (72626 atoms). Deposited as NMRlipids Databank simulation 32 and available from https://doi.org/10.5281/zenodo.3613573. + description: Molecular dynamics trajectory of a lipid bilayer of 460 CLA (43 mol%), + 230 CAL (21 mol%), 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 12 mol%), 128 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 12 mol%) + and 128 SOD (12 mol%) at 298 K. Simulated with Slipids in GROMACS for 1000 ns + (72626 atoms). Deposited as NMRlipids Databank simulation 32 and available from + https://doi.org/10.5281/zenodo.3613573. sameAs: https://doi.org/10.5281/zenodo.3613573 datePublished: '2020-01-13' license: @@ -147,7 +153,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3613573 identifier: 10.5281/zenodo.3613573 url: https://doi.org/10.5281/zenodo.3613573 - name: Simulations of POPC:POPG 1:1 membranes with varying levels of CaCl_2 using the Slipids force field + name: Simulations of POPC:POPG 1:1 membranes with varying levels of CaCl_2 using + the Slipids force field publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/903/468/90346863c8dd3626b433c9f51d06c7d4a263db00/44e1a30df49fd6fafdaa7c1fdeba9a1e215645ad/README.yaml b/Simulations/903/468/90346863c8dd3626b433c9f51d06c7d4a263db00/44e1a30df49fd6fafdaa7c1fdeba9a1e215645ad/README.yaml index 8cf4a04392..3f24e0dd06 100644 --- a/Simulations/903/468/90346863c8dd3626b433c9f51d06c7d4a263db00/44e1a30df49fd6fafdaa7c1fdeba9a1e215645ad/README.yaml +++ b/Simulations/903/468/90346863c8dd3626b433c9f51d06c7d4a263db00/44e1a30df49fd6fafdaa7c1fdeba9a1e215645ad/README.yaml @@ -40,9 +40,12 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 105 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC bilayer at 328 K (CHARMM36, GROMACS 2016.4, 50 ns) [NMRlipids simulation 105] + name: Molecular dynamics trajectory of a DPPC bilayer at 328 K (CHARMM36, GROMACS + 2016.4, 50 ns) [NMRlipids simulation 105] alternateName: 212DPPC_29826SOL_328K - description: Molecular dynamics trajectory of a lipid bilayer of 212 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) at 328 K. Simulated with CHARMM36 in GROMACS 2016.4 for 50 ns (117038 atoms). Deposited as NMRlipids Databank simulation 105 and available from https://doi.org/10.5281/zenodo.3950029. + description: Molecular dynamics trajectory of a lipid bilayer of 212 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) + at 328 K. Simulated with CHARMM36 in GROMACS 2016.4 for 50 ns (117038 atoms). + Deposited as NMRlipids Databank simulation 105 and available from https://doi.org/10.5281/zenodo.3950029. sameAs: https://doi.org/10.5281/zenodo.3950029 datePublished: '2020-07-20' license: @@ -142,7 +145,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3950029 identifier: 10.5281/zenodo.3950029 url: https://doi.org/10.5281/zenodo.3950029 - name: 212 DPPC Molecules bilayer in pure Water, simulated at temperatures ranging from 288K to 358K + name: 212 DPPC Molecules bilayer in pure Water, simulated at temperatures ranging + from 288K to 358K publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/90f/90b/90f90b7a9097418bd99f312299cf76f3ca86e403/e6620192a44308917b63dd11a7e7c34c1c8aa131/README.yaml b/Simulations/90f/90b/90f90b7a9097418bd99f312299cf76f3ca86e403/e6620192a44308917b63dd11a7e7c34c1c8aa131/README.yaml index 28e11bf0c9..6190d0243a 100644 --- a/Simulations/90f/90b/90f90b7a9097418bd99f312299cf76f3ca86e403/e6620192a44308917b63dd11a7e7c34c1c8aa131/README.yaml +++ b/Simulations/90f/90b/90f90b7a9097418bd99f312299cf76f3ca86e403/e6620192a44308917b63dd11a7e7c34c1c8aa131/README.yaml @@ -43,9 +43,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 40 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 310.15 K (CHARMM36 noNBFIX, GROMACS, 383 ns) [NMRlipids simulation 40] + name: Molecular dynamics trajectory of a POPC bilayer at 310.15 K (CHARMM36 noNBFIX, + GROMACS, 383 ns) [NMRlipids simulation 40] alternateName: 200POPC_9000SOL_310K_noNBFIX - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 310.15 K. Simulated with CHARMM36 noNBFIX in GROMACS for 383 ns (53800 atoms). Deposited as NMRlipids Databank simulation 40 and available from https://doi.org/10.5281/zenodo.3434396. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 310.15 K. Simulated with CHARMM36 noNBFIX in GROMACS for 383 ns (53800 atoms). + Deposited as NMRlipids Databank simulation 40 and available from https://doi.org/10.5281/zenodo.3434396. sameAs: https://doi.org/10.5281/zenodo.3434396 datePublished: '2019-09-17' license: diff --git a/Simulations/918/0f6/9180f62aba7690499dbbfdc58115559fdda30cca/5e0b5826edcd12873b603e59a42795c3d0cb6272/README.yaml b/Simulations/918/0f6/9180f62aba7690499dbbfdc58115559fdda30cca/5e0b5826edcd12873b603e59a42795c3d0cb6272/README.yaml index 7f75dbe96f..ee1c9e154d 100644 --- a/Simulations/918/0f6/9180f62aba7690499dbbfdc58115559fdda30cca/5e0b5826edcd12873b603e59a42795c3d0cb6272/README.yaml +++ b/Simulations/918/0f6/9180f62aba7690499dbbfdc58115559fdda30cca/5e0b5826edcd12873b603e59a42795c3d0cb6272/README.yaml @@ -49,9 +49,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/3 ID: 680 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (89:11) bilayer at 298.15 K (Lipid17, GROMACS 2021, 1001 ns) [NMRlipids simulation 680] + name: Molecular dynamics trajectory of a POPC/CHOL (89:11) bilayer at 298.15 K (Lipid17, + GROMACS 2021, 1001 ns) [NMRlipids simulation 680] alternateName: Lipid17_POPC_CHOL11_S - description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 89 mol%) and 8 CHOL (cholesterol, 11 mol%) at 298.15 K. Simulated with Lipid17 in GROMACS 2021 for 1001 ns (19968 atoms). Deposited as NMRlipids Databank simulation 680 and available from https://doi.org/10.5281/zenodo.6992065. + description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 89 mol%) and 8 CHOL (cholesterol, 11 mol%) at 298.15 K. Simulated with Lipid17 + in GROMACS 2021 for 1001 ns (19968 atoms). Deposited as NMRlipids Databank simulation + 680 and available from https://doi.org/10.5281/zenodo.6992065. sameAs: https://doi.org/10.5281/zenodo.6992065 datePublished: '2022-08-15' license: diff --git a/Simulations/91d/151/91d151c45786ce0d4f6d086ce0bb4823b6162a76/13fa4cff572014f6997657c36664f3b6e8daa8d3/README.yaml b/Simulations/91d/151/91d151c45786ce0d4f6d086ce0bb4823b6162a76/13fa4cff572014f6997657c36664f3b6e8daa8d3/README.yaml index 890635bfe4..72d2cfb2e1 100644 --- a/Simulations/91d/151/91d151c45786ce0d4f6d086ce0bb4823b6162a76/13fa4cff572014f6997657c36664f3b6e8daa8d3/README.yaml +++ b/Simulations/91d/151/91d151c45786ce0d4f6d086ce0bb4823b6162a76/13fa4cff572014f6997657c36664f3b6e8daa8d3/README.yaml @@ -51,9 +51,14 @@ EXPERIMENT: POPS: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a CLA/POPC/CAL/POPS/SOD (39:30:19:6:6) bilayer at 298 K (prosECCo75, GROMACS, 500 ns) [NMRlipids simulation 921] + name: Molecular dynamics trajectory of a CLA/POPC/CAL/POPS/SOD (39:30:19:6:6) bilayer + at 298 K (prosECCo75, GROMACS, 500 ns) [NMRlipids simulation 921] alternateName: POPC_60_POPS_12_Na_contraions_600mM_CaCl_prosECCo75 - description: Molecular dynamics trajectory of a lipid bilayer of 78 CLA (39 mol%), 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 30 mol%), 39 CAL (19 mol%), 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 6 mol%) and 12 SOD (6 mol%) at 298 K. Simulated with prosECCo75 in GROMACS for 500 ns (20142 atoms). Deposited as NMRlipids Databank simulation 921 and available from https://doi.org/10.5281/zenodo.22030946. + description: Molecular dynamics trajectory of a lipid bilayer of 78 CLA (39 mol%), + 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 30 mol%), 39 CAL (19 + mol%), 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 6 mol%) and + 12 SOD (6 mol%) at 298 K. Simulated with prosECCo75 in GROMACS for 500 ns (20142 + atoms). Deposited as NMRlipids Databank simulation 921 and available from https://doi.org/10.5281/zenodo.22030946. sameAs: https://doi.org/10.5281/zenodo.22030946 datePublished: '2026-08-20' license: diff --git a/Simulations/91e/760/91e760dc9152050b36f40022035bc0178040d192/8c2cc9f118f1bf5ce65f8ca09ea32346723d3385/README.yaml b/Simulations/91e/760/91e760dc9152050b36f40022035bc0178040d192/8c2cc9f118f1bf5ce65f8ca09ea32346723d3385/README.yaml index 4d0b4336d6..52137774ab 100644 --- a/Simulations/91e/760/91e760dc9152050b36f40022035bc0178040d192/8c2cc9f118f1bf5ce65f8ca09ea32346723d3385/README.yaml +++ b/Simulations/91e/760/91e760dc9152050b36f40022035bc0178040d192/8c2cc9f118f1bf5ce65f8ca09ea32346723d3385/README.yaml @@ -48,9 +48,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 383 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (48:35:17) bilayer at 310.15 K (ECC-CHARMM36, GROMACS 5.1.4, 614 ns) [NMRlipids simulation 383] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (48:35:17) bilayer at 310.15 + K (ECC-CHARMM36, GROMACS 5.1.4, 614 ns) [NMRlipids simulation 383] alternateName: 200POPC_9000SOL_73CAL_146CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 48 mol%), 146 CLA (35 mol%) and 73 CAL (17 mol%) at 310.15 K. Simulated with ECC-CHARMM36 in GROMACS 5.1.4 for 614 ns (54019 atoms). Deposited as NMRlipids Databank simulation 383 and available from https://doi.org/10.5281/zenodo.2562079. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 48 mol%), 146 CLA (35 mol%) and 73 CAL (17 mol%) at 310.15 K. Simulated with ECC-CHARMM36 + in GROMACS 5.1.4 for 614 ns (54019 atoms). Deposited as NMRlipids Databank simulation + 383 and available from https://doi.org/10.5281/zenodo.2562079. sameAs: https://doi.org/10.5281/zenodo.2562079 datePublished: '2019-02-11' license: @@ -138,7 +142,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.2562079 identifier: 10.5281/zenodo.2562079 url: https://doi.org/10.5281/zenodo.2562079 - name: Simulation data for ECC-CHARMM36 POPC bilayer, 100 lipids/leaflet, 450 mM CaCl2, 310K, GROMACS 5.1.4 + name: Simulation data for ECC-CHARMM36 POPC bilayer, 100 lipids/leaflet, 450 mM + CaCl2, 310K, GROMACS 5.1.4 publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/920/e99/920e9922bb4525d4634d704ca132b70fec41efb0/72afd68d9748c1a9e44512a53737fabc542f09a6/README.yaml b/Simulations/920/e99/920e9922bb4525d4634d704ca132b70fec41efb0/72afd68d9748c1a9e44512a53737fabc542f09a6/README.yaml index 9b3fd8ca4f..33bb5a2a19 100644 --- a/Simulations/920/e99/920e9922bb4525d4634d704ca132b70fec41efb0/72afd68d9748c1a9e44512a53737fabc542f09a6/README.yaml +++ b/Simulations/920/e99/920e9922bb4525d4634d704ca132b70fec41efb0/72afd68d9748c1a9e44512a53737fabc542f09a6/README.yaml @@ -39,9 +39,12 @@ EXPERIMENT: - 10.1021/acs.jpcb.4c04719/1 FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 300 K (Charmm36, GROMACS 2019.5, 650 ns) [NMRlipids simulation 795] + name: Molecular dynamics trajectory of a POPC bilayer at 300 K (Charmm36, GROMACS + 2019.5, 650 ns) [NMRlipids simulation 795] alternateName: POPС(300K, 5w/l, CHARMM36) - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 300 K. Simulated with Charmm36 in GROMACS 2019.5 for 650 ns (29800 atoms). Deposited as NMRlipids Databank simulation 795 and available from https://doi.org/10.5281/zenodo.6333548. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 300 K. Simulated with Charmm36 in GROMACS 2019.5 for 650 ns (29800 atoms). + Deposited as NMRlipids Databank simulation 795 and available from https://doi.org/10.5281/zenodo.6333548. sameAs: https://doi.org/10.5281/zenodo.6333548 datePublished: '2022-03-07' license: diff --git a/Simulations/921/090/921090f8f1701f357b74eb0ca6ac3b97299bc75f/f9b367c920ac1ad66a9a7ab9958d19218f50019e/README.yaml b/Simulations/921/090/921090f8f1701f357b74eb0ca6ac3b97299bc75f/f9b367c920ac1ad66a9a7ab9958d19218f50019e/README.yaml index 8ac3c6e730..240da4dfd6 100644 --- a/Simulations/921/090/921090f8f1701f357b74eb0ca6ac3b97299bc75f/f9b367c920ac1ad66a9a7ab9958d19218f50019e/README.yaml +++ b/Simulations/921/090/921090f8f1701f357b74eb0ca6ac3b97299bc75f/f9b367c920ac1ad66a9a7ab9958d19218f50019e/README.yaml @@ -47,9 +47,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 863 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (81:13:6) bilayer at 300 K (OPLS3e, GROMACS Desmond of Schrödinger 2019-4, 243 ns) [NMRlipids simulation 863] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (81:13:6) bilayer at 300 K + (OPLS3e, GROMACS Desmond of Schrödinger 2019-4, 243 ns) [NMRlipids simulation + 863] alternateName: POPC, 44 w/l, 300 K, 0.1 M CaCl2 - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 81 mol%), 32 CLA (13 mol%) and 16 CAL (6 mol%) at 300 K. Simulated with OPLS3e in GROMACS Desmond of Schrödinger 2019-4 for 243 ns (53488 atoms). Deposited as NMRlipids Databank simulation 863 and available from https://doi.org/10.5281/zenodo.10212636. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 81 mol%), 32 CLA (13 mol%) and 16 CAL (6 mol%) at 300 K. Simulated with OPLS3e + in GROMACS Desmond of Schrödinger 2019-4 for 243 ns (53488 atoms). Deposited as + NMRlipids Databank simulation 863 and available from https://doi.org/10.5281/zenodo.10212636. sameAs: https://doi.org/10.5281/zenodo.10212636 datePublished: '2022' license: @@ -140,7 +145,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.10212636 identifier: 10.5281/zenodo.10212636 url: https://doi.org/10.5281/zenodo.10212636 - name: MD simulation of POPC bilayer with OPLS3e force field, 100 mM CaCl2 part 1 + name: MD simulation of POPC bilayer with OPLS3e force field, 100 mM CaCl2 part + 1 publisher: Zenodo _source: api: datacite diff --git a/Simulations/924/ea6/924ea67948ef064e85991f142a5e2388af6296b4/c2626917d469d7e2818613569ed95c834174c82c/README.yaml b/Simulations/924/ea6/924ea67948ef064e85991f142a5e2388af6296b4/c2626917d469d7e2818613569ed95c834174c82c/README.yaml index 4eef419b44..47901168ed 100644 --- a/Simulations/924/ea6/924ea67948ef064e85991f142a5e2388af6296b4/c2626917d469d7e2818613569ed95c834174c82c/README.yaml +++ b/Simulations/924/ea6/924ea67948ef064e85991f142a5e2388af6296b4/c2626917d469d7e2818613569ed95c834174c82c/README.yaml @@ -44,9 +44,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 77 bioschema_properties: - name: Molecular dynamics trajectory of a DOPE bilayer at 271 K (Berger-DOPE-2004, GROMACS 4.0.7, 100 ns) [NMRlipids simulation 77] + name: Molecular dynamics trajectory of a DOPE bilayer at 271 K (Berger-DOPE-2004, + GROMACS 4.0.7, 100 ns) [NMRlipids simulation 77] alternateName: 128DOPE_4789SOL_271K_v1 - description: Molecular dynamics trajectory of a lipid bilayer of 128 DOPE (1,2-dioleoyl-sn-glycero-3-phosphoethanolamine) at 271 K. Simulated with Berger-DOPE-2004 in GROMACS 4.0.7 for 100 ns (21279 atoms). Deposited as NMRlipids Databank simulation 77 and available from https://doi.org/10.5281/zenodo.1293928. + description: Molecular dynamics trajectory of a lipid bilayer of 128 DOPE (1,2-dioleoyl-sn-glycero-3-phosphoethanolamine) + at 271 K. Simulated with Berger-DOPE-2004 in GROMACS 4.0.7 for 100 ns (21279 atoms). + Deposited as NMRlipids Databank simulation 77 and available from https://doi.org/10.5281/zenodo.1293928. sameAs: https://doi.org/10.5281/zenodo.1293928 datePublished: '2018-06-20' license: diff --git a/Simulations/92b/b78/92bb78fa030c101f9a684e523e010dc1f1358a9e/56ef975f609cc342145b12c14ac8b68079849c00/README.yaml b/Simulations/92b/b78/92bb78fa030c101f9a684e523e010dc1f1358a9e/56ef975f609cc342145b12c14ac8b68079849c00/README.yaml index fd074653a5..1c086ccfdd 100644 --- a/Simulations/92b/b78/92bb78fa030c101f9a684e523e010dc1f1358a9e/56ef975f609cc342145b12c14ac8b68079849c00/README.yaml +++ b/Simulations/92b/b78/92bb78fa030c101f9a684e523e010dc1f1358a9e/56ef975f609cc342145b12c14ac8b68079849c00/README.yaml @@ -41,9 +41,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 385 bioschema_properties: - name: Molecular dynamics trajectory of a POPE bilayer at 300 K (MacRog, GROMACS, 500 ns) [NMRlipids simulation 385] + name: Molecular dynamics trajectory of a POPE bilayer at 300 K (MacRog, GROMACS, + 500 ns) [NMRlipids simulation 385] alternateName: 128POPE_5120SOL_300K - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) at 300 K. Simulated with MacRog in GROMACS for 500 ns (31360 atoms). Deposited as NMRlipids Databank simulation 385 and available from https://doi.org/10.5281/zenodo.3725670. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) + at 300 K. Simulated with MacRog in GROMACS for 500 ns (31360 atoms). Deposited + as NMRlipids Databank simulation 385 and available from https://doi.org/10.5281/zenodo.3725670. sameAs: https://doi.org/10.5281/zenodo.3725670 datePublished: '2020-03-26' license: diff --git a/Simulations/92e/b2d/92eb2d09d236241f97d6102bf3c32868d2fd9cdf/47cd801878d9871123ce54de5f03cd0dc0c4d17f/README.yaml b/Simulations/92e/b2d/92eb2d09d236241f97d6102bf3c32868d2fd9cdf/47cd801878d9871123ce54de5f03cd0dc0c4d17f/README.yaml index 0f4fb7835a..97eb0235fc 100644 --- a/Simulations/92e/b2d/92eb2d09d236241f97d6102bf3c32868d2fd9cdf/47cd801878d9871123ce54de5f03cd0dc0c4d17f/README.yaml +++ b/Simulations/92e/b2d/92eb2d09d236241f97d6102bf3c32868d2fd9cdf/47cd801878d9871123ce54de5f03cd0dc0c4d17f/README.yaml @@ -49,9 +49,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/3 ID: 681 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (89:11) bilayer at 298.15 K (Slipids, GROMACS 2021, 1001 ns) [NMRlipids simulation 681] + name: Molecular dynamics trajectory of a POPC/CHOL (89:11) bilayer at 298.15 K (Slipids, + GROMACS 2021, 1001 ns) [NMRlipids simulation 681] alternateName: Slipids_POPC_CHOL11_M - description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 89 mol%) and 32 CHOL (cholesterol, 11 mol%) at 298.15 K. Simulated with Slipids in GROMACS 2021 for 1001 ns (79872 atoms). Deposited as NMRlipids Databank simulation 681 and available from https://doi.org/10.5281/zenodo.7022749. + description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 89 mol%) and 32 CHOL (cholesterol, 11 mol%) at 298.15 K. Simulated with Slipids + in GROMACS 2021 for 1001 ns (79872 atoms). Deposited as NMRlipids Databank simulation + 681 and available from https://doi.org/10.5281/zenodo.7022749. sameAs: https://doi.org/10.5281/zenodo.7022749 datePublished: '2022-08-23' license: diff --git a/Simulations/92f/99b/92f99b3fdbed01824af994eeb0b4bd62529784ab/92f99b3fdbed01824af994eeb0b4bd62529784ab/README.yaml b/Simulations/92f/99b/92f99b3fdbed01824af994eeb0b4bd62529784ab/92f99b3fdbed01824af994eeb0b4bd62529784ab/README.yaml index 402784c4f3..85edeefd0e 100644 --- a/Simulations/92f/99b/92f99b3fdbed01824af994eeb0b4bd62529784ab/92f99b3fdbed01824af994eeb0b4bd62529784ab/README.yaml +++ b/Simulations/92f/99b/92f99b3fdbed01824af994eeb0b4bd62529784ab/92f99b3fdbed01824af994eeb0b4bd62529784ab/README.yaml @@ -37,9 +37,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 746 bioschema_properties: - name: Molecular dynamics trajectory of a POPE bilayer at 303 K (AMOEBA, OPENMM v7.5.1, 306 ns) [NMRlipids simulation 746] + name: Molecular dynamics trajectory of a POPE bilayer at 303 K (AMOEBA, OPENMM v7.5.1, + 306 ns) [NMRlipids simulation 746] alternateName: POPE_nosalt_at_303K_with_AMOEBA - description: Molecular dynamics trajectory of a lipid bilayer of 72 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) at 303 K. Simulated with AMOEBA in OPENMM v7.5.1 for 306 ns (17640 atoms). Deposited as NMRlipids Databank simulation 746 and available from https://doi.org/10.5281/zenodo.7622838. + description: Molecular dynamics trajectory of a lipid bilayer of 72 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) + at 303 K. Simulated with AMOEBA in OPENMM v7.5.1 for 306 ns (17640 atoms). Deposited + as NMRlipids Databank simulation 746 and available from https://doi.org/10.5281/zenodo.7622838. sameAs: https://doi.org/10.5281/zenodo.7622838 datePublished: '2023-02-08' license: diff --git a/Simulations/933/d66/933d66dc22f3196b8d56e067fc9ca51ad41b3421/3165c6c4e946e82550cde8d754a8260961652f5b/README.yaml b/Simulations/933/d66/933d66dc22f3196b8d56e067fc9ca51ad41b3421/3165c6c4e946e82550cde8d754a8260961652f5b/README.yaml index 410bfcde61..05a3c0b61c 100644 --- a/Simulations/933/d66/933d66dc22f3196b8d56e067fc9ca51ad41b3421/3165c6c4e946e82550cde8d754a8260961652f5b/README.yaml +++ b/Simulations/933/d66/933d66dc22f3196b8d56e067fc9ca51ad41b3421/3165c6c4e946e82550cde8d754a8260961652f5b/README.yaml @@ -49,9 +49,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 192 bioschema_properties: - name: Molecular dynamics trajectory of a DSPC/CLA/SOD (82:9:9) bilayer at 333 K (CHARMM36, GROMACS 5.0.4, 640 ns) [NMRlipids simulation 192] + name: Molecular dynamics trajectory of a DSPC/CLA/SOD (82:9:9) bilayer at 333 K + (CHARMM36, GROMACS 5.0.4, 640 ns) [NMRlipids simulation 192] alternateName: 512DSPC_20480SOL_55SOD_55CLA_333K - description: Molecular dynamics trajectory of a lipid bilayer of 512 DSPC (1,2-distearoyl-sn-glycero-3-phosphocholine, 82 mol%), 55 CLA (9 mol%) and 55 SOD (9 mol%) at 333 K. Simulated with CHARMM36 in GROMACS 5.0.4 for 640 ns (134254 atoms). Deposited as NMRlipids Databank simulation 192 and available from https://doi.org/10.5281/zenodo.1009094. + description: Molecular dynamics trajectory of a lipid bilayer of 512 DSPC (1,2-distearoyl-sn-glycero-3-phosphocholine, + 82 mol%), 55 CLA (9 mol%) and 55 SOD (9 mol%) at 333 K. Simulated with CHARMM36 + in GROMACS 5.0.4 for 640 ns (134254 atoms). Deposited as NMRlipids Databank simulation + 192 and available from https://doi.org/10.5281/zenodo.1009094. sameAs: https://doi.org/10.5281/zenodo.1009094 datePublished: '2017-10-11' license: diff --git a/Simulations/937/79c/93779c1aa60f5e4b879c8b6e0d803bb01a127fc6/3e259f4c7f19eff23390fc96c7fb22485b8518e4/README.yaml b/Simulations/937/79c/93779c1aa60f5e4b879c8b6e0d803bb01a127fc6/3e259f4c7f19eff23390fc96c7fb22485b8518e4/README.yaml index 9cdac29b92..eb7b207cc4 100644 --- a/Simulations/937/79c/93779c1aa60f5e4b879c8b6e0d803bb01a127fc6/3e259f4c7f19eff23390fc96c7fb22485b8518e4/README.yaml +++ b/Simulations/937/79c/93779c1aa60f5e4b879c8b6e0d803bb01a127fc6/3e259f4c7f19eff23390fc96c7fb22485b8518e4/README.yaml @@ -54,9 +54,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 273 bioschema_properties: - name: Molecular dynamics trajectory of a CLA/POPC/CAL (48:28:24) bilayer at 313 K (ECC-lipids, GROMACS 5.1.4, 300 ns) [NMRlipids simulation 273] + name: Molecular dynamics trajectory of a CLA/POPC/CAL (48:28:24) bilayer at 313 + K (ECC-lipids, GROMACS 5.1.4, 300 ns) [NMRlipids simulation 273] alternateName: 128POPC_6232SOL_110CAL_220CLA_313K_TIP3pmodel - description: Molecular dynamics trajectory of a lipid bilayer of 220 CLA (48 mol%), 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 28 mol%) and 110 CAL (24 mol%) at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 300 ns (36178 atoms). Deposited as NMRlipids Databank simulation 273 and available from https://doi.org/10.5281/zenodo.1118980. + description: Molecular dynamics trajectory of a lipid bilayer of 220 CLA (48 mol%), + 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 28 mol%) and 110 CAL + (24 mol%) at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 300 ns (36178 + atoms). Deposited as NMRlipids Databank simulation 273 and available from https://doi.org/10.5281/zenodo.1118980. sameAs: https://doi.org/10.5281/zenodo.1118980 datePublished: '2017-12-19' license: @@ -146,7 +150,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1118980 identifier: 10.5281/zenodo.1118980 url: https://doi.org/10.5281/zenodo.1118980 - name: Simulations Of Popc Lipid Bilayer In Water Solution At Various Nacl And Cacl2 Concentrations Using Ecc-Popc Force Field And Various Water Models + name: Simulations Of Popc Lipid Bilayer In Water Solution At Various Nacl And + Cacl2 Concentrations Using Ecc-Popc Force Field And Various Water Models publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/939/034/939034209c124cb6cb99baf9f942adb2d65d44de/ca780a3c0bbfe18d17e0dc480a4f71520f70eca9/README.yaml b/Simulations/939/034/939034209c124cb6cb99baf9f942adb2d65d44de/ca780a3c0bbfe18d17e0dc480a4f71520f70eca9/README.yaml index b34c11ed08..954aee32fb 100644 --- a/Simulations/939/034/939034209c124cb6cb99baf9f942adb2d65d44de/ca780a3c0bbfe18d17e0dc480a4f71520f70eca9/README.yaml +++ b/Simulations/939/034/939034209c124cb6cb99baf9f942adb2d65d44de/ca780a3c0bbfe18d17e0dc480a4f71520f70eca9/README.yaml @@ -46,9 +46,14 @@ EXPERIMENT: - 10.1016/j.bbamem.2011.07.022/4 ID: 545 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC bilayer at 323 K (Poger GROMOS 53A6_L; Reaction Field for computing electrostatics, GROMACS 4.0.7, 100 ns) [NMRlipids simulation 545] + name: Molecular dynamics trajectory of a DPPC bilayer at 323 K (Poger GROMOS 53A6_L; + Reaction Field for computing electrostatics, GROMACS 4.0.7, 100 ns) [NMRlipids + simulation 545] alternateName: 128DPPC_5841SOL_323K - description: Molecular dynamics trajectory of a lipid bilayer of 128 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) at 323 K. Simulated with Poger GROMOS 53A6_L; Reaction Field for computing electrostatics in GROMACS 4.0.7 for 100 ns (23923 atoms). Deposited as NMRlipids Databank simulation 545 and available from https://doi.org/10.5281/zenodo.14591. + description: Molecular dynamics trajectory of a lipid bilayer of 128 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) + at 323 K. Simulated with Poger GROMOS 53A6_L; Reaction Field for computing electrostatics + in GROMACS 4.0.7 for 100 ns (23923 atoms). Deposited as NMRlipids Databank simulation + 545 and available from https://doi.org/10.5281/zenodo.14591. sameAs: https://doi.org/10.5281/zenodo.14591 datePublished: '2015-01-26' license: @@ -140,7 +145,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.14591 identifier: 10.5281/zenodo.14591 url: https://doi.org/10.5281/zenodo.14591 - name: Md Simulation Trajectory And Related Files For Dppc Bilayer In Full Hydration (Poger Gromos 53A6_L, Gromacs 4.0.7, Reaction Field, Traj 2) + name: Md Simulation Trajectory And Related Files For Dppc Bilayer In Full Hydration + (Poger Gromos 53A6_L, Gromacs 4.0.7, Reaction Field, Traj 2) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/93f/385/93f3857977ebbdf869cd4457fbfad82f48e8f304/797a337035d641067dadb714f6fc7cc40a2bcccc/README.yaml b/Simulations/93f/385/93f3857977ebbdf869cd4457fbfad82f48e8f304/797a337035d641067dadb714f6fc7cc40a2bcccc/README.yaml index 054d574782..4fe61645e3 100644 --- a/Simulations/93f/385/93f3857977ebbdf869cd4457fbfad82f48e8f304/797a337035d641067dadb714f6fc7cc40a2bcccc/README.yaml +++ b/Simulations/93f/385/93f3857977ebbdf869cd4457fbfad82f48e8f304/797a337035d641067dadb714f6fc7cc40a2bcccc/README.yaml @@ -46,9 +46,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 118 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (70:30) bilayer at 298 K (Slipids, GROMACS 4.6.3, 100 ns) [NMRlipids simulation 118] + name: Molecular dynamics trajectory of a POPC/CHOL (70:30) bilayer at 298 K (Slipids, + GROMACS 4.6.3, 100 ns) [NMRlipids simulation 118] alternateName: 154CHOL_358POPC_21183SOL_298K - description: Molecular dynamics trajectory of a lipid bilayer of 358 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 70 mol%) and 154 CHOL (cholesterol, 30 mol%) at 298 K. Simulated with Slipids in GROMACS 4.6.3 for 100 ns (122917 atoms). Deposited as NMRlipids Databank simulation 118 and available from https://doi.org/10.5281/zenodo.62026. + description: Molecular dynamics trajectory of a lipid bilayer of 358 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 70 mol%) and 154 CHOL (cholesterol, 30 mol%) at 298 K. Simulated with Slipids + in GROMACS 4.6.3 for 100 ns (122917 atoms). Deposited as NMRlipids Databank simulation + 118 and available from https://doi.org/10.5281/zenodo.62026. sameAs: https://doi.org/10.5281/zenodo.62026 datePublished: '2016-09-10' license: @@ -137,7 +141,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.62026 identifier: 10.5281/zenodo.62026 url: https://doi.org/10.5281/zenodo.62026 - name: 'Md Simulation Trajectory Of A Lipid Bilayer: 70/30 Mol% Popc/Cholesterol . Slipids, Gromacs 4.6.3. 2016.' + name: 'Md Simulation Trajectory Of A Lipid Bilayer: 70/30 Mol% Popc/Cholesterol + . Slipids, Gromacs 4.6.3. 2016.' publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/944/25d/94425d6fcd0a0716ffd72d8908daff83a5ec6772/db9102a50e078ee7769b908aef3ad900f9172ae4/README.yaml b/Simulations/944/25d/94425d6fcd0a0716ffd72d8908daff83a5ec6772/db9102a50e078ee7769b908aef3ad900f9172ae4/README.yaml index 890e0df753..48c26a5657 100644 --- a/Simulations/944/25d/94425d6fcd0a0716ffd72d8908daff83a5ec6772/db9102a50e078ee7769b908aef3ad900f9172ae4/README.yaml +++ b/Simulations/944/25d/94425d6fcd0a0716ffd72d8908daff83a5ec6772/db9102a50e078ee7769b908aef3ad900f9172ae4/README.yaml @@ -54,9 +54,14 @@ DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 538 AUTHORS_CONTACT: Javanainen, Matti bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPG/SOD/CLA/CAL (25:25:25:18:9) bilayer at 298 K (Slipids, GROMACS, 1000 ns) [NMRlipids simulation 538] + name: Molecular dynamics trajectory of a POPC/POPG/SOD/CLA/CAL (25:25:25:18:9) bilayer + at 298 K (Slipids, GROMACS, 1000 ns) [NMRlipids simulation 538] alternateName: POPCPOPG(1:1)200mMCaCl2 - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 25 mol%), 128 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 25 mol%), 128 SOD (25 mol%), 92 CLA (18 mol%) and 46 CAL (9 mol%) at 298 K. Simulated with Slipids in GROMACS for 1000 ns (72074 atoms). Deposited as NMRlipids Databank simulation 538 and available from https://doi.org/10.5281/zenodo.3613573. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 25 mol%), 128 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 25 mol%), + 128 SOD (25 mol%), 92 CLA (18 mol%) and 46 CAL (9 mol%) at 298 K. Simulated with + Slipids in GROMACS for 1000 ns (72074 atoms). Deposited as NMRlipids Databank + simulation 538 and available from https://doi.org/10.5281/zenodo.3613573. sameAs: https://doi.org/10.5281/zenodo.3613573 datePublished: '2020-01-13' license: @@ -147,7 +152,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3613573 identifier: 10.5281/zenodo.3613573 url: https://doi.org/10.5281/zenodo.3613573 - name: Simulations of POPC:POPG 1:1 membranes with varying levels of CaCl_2 using the Slipids force field + name: Simulations of POPC:POPG 1:1 membranes with varying levels of CaCl_2 using + the Slipids force field publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/946/cf2/946cf2f5d93a308dea838474fb3ec0492cdbf284/55289dc7b77f58d97beb5d6e3506a9e6f2d9256e/README.yaml b/Simulations/946/cf2/946cf2f5d93a308dea838474fb3ec0492cdbf284/55289dc7b77f58d97beb5d6e3506a9e6f2d9256e/README.yaml index 17b7184d3c..c71a446997 100644 --- a/Simulations/946/cf2/946cf2f5d93a308dea838474fb3ec0492cdbf284/55289dc7b77f58d97beb5d6e3506a9e6f2d9256e/README.yaml +++ b/Simulations/946/cf2/946cf2f5d93a308dea838474fb3ec0492cdbf284/55289dc7b77f58d97beb5d6e3506a9e6f2d9256e/README.yaml @@ -40,9 +40,12 @@ EXPERIMENT: FORMFACTOR: - 10.1021/acs.jctc.3c00648/1 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 300 K (OpenFF, GROMACS, 200 ns) [NMRlipids simulation 761] + name: Molecular dynamics trajectory of a POPC bilayer at 300 K (OpenFF, GROMACS, + 200 ns) [NMRlipids simulation 761] alternateName: POPC_128_OPENFF_300K - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 300 K. Simulated with OpenFF in GROMACS for 200 ns (32152 atoms). Deposited as NMRlipids Databank simulation 761 and available from https://doi.org/10.5281/zenodo.8299506. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 300 K. Simulated with OpenFF in GROMACS for 200 ns (32152 atoms). Deposited + as NMRlipids Databank simulation 761 and available from https://doi.org/10.5281/zenodo.8299506. sameAs: https://doi.org/10.5281/zenodo.8299506 datePublished: '2023-08-29' license: diff --git a/Simulations/94c/502/94c50221771bf554ddf1ed9d68043f164258cae2/d1149b77cf5532ceb124f393a96b9c766888265c/README.yaml b/Simulations/94c/502/94c50221771bf554ddf1ed9d68043f164258cae2/d1149b77cf5532ceb124f393a96b9c766888265c/README.yaml index c31334b0cb..06e1773610 100644 --- a/Simulations/94c/502/94c50221771bf554ddf1ed9d68043f164258cae2/d1149b77cf5532ceb124f393a96b9c766888265c/README.yaml +++ b/Simulations/94c/502/94c50221771bf554ddf1ed9d68043f164258cae2/d1149b77cf5532ceb124f393a96b9c766888265c/README.yaml @@ -50,9 +50,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 298 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (71:29) bilayer at 298.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 298] + name: Molecular dynamics trajectory of a POPC/CHOL (71:29) bilayer at 298.15 K (CHARMM36, + GROMACS, 1001 ns) [NMRlipids simulation 298] alternateName: 256POPC_104CHOL_18000SOL_298K - description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 71 mol%) and 104 CHOL (cholesterol, 29 mol%) at 298.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (96000 atoms). Deposited as NMRlipids Databank simulation 298 and available from https://doi.org/10.5281/zenodo.5767451. + description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 71 mol%) and 104 CHOL (cholesterol, 29 mol%) at 298.15 K. Simulated with CHARMM36 + in GROMACS for 1001 ns (96000 atoms). Deposited as NMRlipids Databank simulation + 298 and available from https://doi.org/10.5281/zenodo.5767451. sameAs: https://doi.org/10.5281/zenodo.5767451 datePublished: '2021-12-08' license: diff --git a/Simulations/954/9cc/9549cc0d99530a33f0198dc6478b25fd33e67353/2f29dd26de3bf65ccb9a8785141dd44e5eb7c660/README.yaml b/Simulations/954/9cc/9549cc0d99530a33f0198dc6478b25fd33e67353/2f29dd26de3bf65ccb9a8785141dd44e5eb7c660/README.yaml index 6fff7e2392..5683a45532 100644 --- a/Simulations/954/9cc/9549cc0d99530a33f0198dc6478b25fd33e67353/2f29dd26de3bf65ccb9a8785141dd44e5eb7c660/README.yaml +++ b/Simulations/954/9cc/9549cc0d99530a33f0198dc6478b25fd33e67353/2f29dd26de3bf65ccb9a8785141dd44e5eb7c660/README.yaml @@ -51,9 +51,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/3 ID: 119 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (89:11) bilayer at 298.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 119] + name: Molecular dynamics trajectory of a POPC/CHOL (89:11) bilayer at 298.15 K (CHARMM36, + GROMACS, 1001 ns) [NMRlipids simulation 119] alternateName: 256POPC_32CHOL_14400SOL_298K - description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 89 mol%) and 32 CHOL (cholesterol, 11 mol%) at 298.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (79872 atoms). Deposited as NMRlipids Databank simulation 119 and available from https://doi.org/10.5281/zenodo.5767451. + description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 89 mol%) and 32 CHOL (cholesterol, 11 mol%) at 298.15 K. Simulated with CHARMM36 + in GROMACS for 1001 ns (79872 atoms). Deposited as NMRlipids Databank simulation + 119 and available from https://doi.org/10.5281/zenodo.5767451. sameAs: https://doi.org/10.5281/zenodo.5767451 datePublished: '2021-12-08' license: diff --git a/Simulations/95c/736/95c7369066c86ec65669e86bf250814c3bdb6033/0f4d4825670af2e814557030787f14a3f376d6ea/README.yaml b/Simulations/95c/736/95c7369066c86ec65669e86bf250814c3bdb6033/0f4d4825670af2e814557030787f14a3f376d6ea/README.yaml index d99e860be8..a53d4c3256 100644 --- a/Simulations/95c/736/95c7369066c86ec65669e86bf250814c3bdb6033/0f4d4825670af2e814557030787f14a3f376d6ea/README.yaml +++ b/Simulations/95c/736/95c7369066c86ec65669e86bf250814c3bdb6033/0f4d4825670af2e814557030787f14a3f376d6ea/README.yaml @@ -42,9 +42,12 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 319 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC bilayer at 323 K (CHARMM36, GROMACS 4.5, 25 ns) [NMRlipids simulation 319] + name: Molecular dynamics trajectory of a DPPC bilayer at 323 K (CHARMM36, GROMACS + 4.5, 25 ns) [NMRlipids simulation 319] alternateName: 72DPPC_2189SOL_323K - description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) at 323 K. Simulated with CHARMM36 in GROMACS 4.5 for 25 ns (15927 atoms). Deposited as NMRlipids Databank simulation 319 and available from https://doi.org/10.5281/zenodo.15549. + description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) + at 323 K. Simulated with CHARMM36 in GROMACS 4.5 for 25 ns (15927 atoms). Deposited + as NMRlipids Databank simulation 319 and available from https://doi.org/10.5281/zenodo.15549. sameAs: https://doi.org/10.5281/zenodo.15549 datePublished: '2015-02-20' license: @@ -136,7 +139,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.15549 identifier: 10.5281/zenodo.15549 url: https://doi.org/10.5281/zenodo.15549 - name: Md Simulation Trajectory And Related Files For Dppc Bilayer (Charmm36, Gromacs 4.5) + name: Md Simulation Trajectory And Related Files For Dppc Bilayer (Charmm36, Gromacs + 4.5) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/95e/683/95e683dffe9d844534fe148a22cc902ef4c6d3ce/95e683dffe9d844534fe148a22cc902ef4c6d3ce/README.yaml b/Simulations/95e/683/95e683dffe9d844534fe148a22cc902ef4c6d3ce/95e683dffe9d844534fe148a22cc902ef4c6d3ce/README.yaml index 12ea6d09aa..92d6732e2a 100644 --- a/Simulations/95e/683/95e683dffe9d844534fe148a22cc902ef4c6d3ce/95e683dffe9d844534fe148a22cc902ef4c6d3ce/README.yaml +++ b/Simulations/95e/683/95e683dffe9d844534fe148a22cc902ef4c6d3ce/95e683dffe9d844534fe148a22cc902ef4c6d3ce/README.yaml @@ -38,9 +38,12 @@ EXPERIMENT: FORMFACTOR: - 10.1016/j.chemphyslip.2020.104892/2 bioschema_properties: - name: Molecular dynamics trajectory of a SDPC bilayer at 303.15 K (CHARMM36m, NAMD 3, 500 ns) [NMRlipids simulation 899] + name: Molecular dynamics trajectory of a SDPC bilayer at 303.15 K (CHARMM36m, NAMD + 3, 500 ns) [NMRlipids simulation 899] alternateName: SDPC(18:0(d35)/22:6) - description: Molecular dynamics trajectory of a lipid bilayer of 200 SDPC (1-stearoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine) at 303.15 K. Simulated with CHARMM36m in NAMD 3 for 500 ns (57200 atoms). Deposited as NMRlipids Databank simulation 899 and available from https://doi.org/10.5281/zenodo.18469822. + description: Molecular dynamics trajectory of a lipid bilayer of 200 SDPC (1-stearoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine) + at 303.15 K. Simulated with CHARMM36m in NAMD 3 for 500 ns (57200 atoms). Deposited + as NMRlipids Databank simulation 899 and available from https://doi.org/10.5281/zenodo.18469822. sameAs: https://doi.org/10.5281/zenodo.18469822 datePublished: '2026-02-03' license: @@ -132,7 +135,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.18469822 identifier: 10.5281/zenodo.18469822 url: https://doi.org/10.5281/zenodo.18469822 - name: 1-stearoyl(d35)-2-docosahexaenoyl-sn-glycero-3-phosphocholine (18:0(d35)/22:6n3PC) | SDPC lipid bilayer, 303K, CHARMM36m-WYF forcefield, NAMD 3.0.2, 2* 500 ns + name: 1-stearoyl(d35)-2-docosahexaenoyl-sn-glycero-3-phosphocholine (18:0(d35)/22:6n3PC) + | SDPC lipid bilayer, 303K, CHARMM36m-WYF forcefield, NAMD 3.0.2, 2* 500 ns publisher: Zenodo _source: api: datacite diff --git a/Simulations/96a/292/96a292e484ec84f102f76c87584e373a35688cbe/b5db545685561c065703b359b454484f53c01fe4/README.yaml b/Simulations/96a/292/96a292e484ec84f102f76c87584e373a35688cbe/b5db545685561c065703b359b454484f53c01fe4/README.yaml index 156a6dc99a..80a39daced 100644 --- a/Simulations/96a/292/96a292e484ec84f102f76c87584e373a35688cbe/b5db545685561c065703b359b454484f53c01fe4/README.yaml +++ b/Simulations/96a/292/96a292e484ec84f102f76c87584e373a35688cbe/b5db545685561c065703b359b454484f53c01fe4/README.yaml @@ -43,9 +43,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 476 bioschema_properties: - name: Molecular dynamics trajectory of a DOPS/SOD (50:50) bilayer at 303 K (CHARMM36, GROMACS, 100 ns) [NMRlipids simulation 476] + name: Molecular dynamics trajectory of a DOPS/SOD (50:50) bilayer at 303 K (CHARMM36, + GROMACS, 100 ns) [NMRlipids simulation 476] alternateName: 128DOPS_128SOD_4480SOL_303K_v2 - description: Molecular dynamics trajectory of a lipid bilayer of 128 DOPS (1,2-dioleoyl-sn-glycero-3-phospho-L-serine, 50 mol%) and 128 SOD (50 mol%) at 303 K. Simulated with CHARMM36 in GROMACS for 100 ns (30336 atoms). Deposited as NMRlipids Databank simulation 476 and available from https://doi.org/10.5281/zenodo.1129411. + description: Molecular dynamics trajectory of a lipid bilayer of 128 DOPS (1,2-dioleoyl-sn-glycero-3-phospho-L-serine, + 50 mol%) and 128 SOD (50 mol%) at 303 K. Simulated with CHARMM36 in GROMACS for + 100 ns (30336 atoms). Deposited as NMRlipids Databank simulation 476 and available + from https://doi.org/10.5281/zenodo.1129411. sameAs: https://doi.org/10.5281/zenodo.1129411 datePublished: '2017-12-24' license: diff --git a/Simulations/96f/656/96f65688e4d3d870516abbb3dba34436df44cd52/53cf119244fbdad6b04b8c9cd2d33090afeba06a/README.yaml b/Simulations/96f/656/96f65688e4d3d870516abbb3dba34436df44cd52/53cf119244fbdad6b04b8c9cd2d33090afeba06a/README.yaml index 51592f4b28..826f762d99 100644 --- a/Simulations/96f/656/96f65688e4d3d870516abbb3dba34436df44cd52/53cf119244fbdad6b04b8c9cd2d33090afeba06a/README.yaml +++ b/Simulations/96f/656/96f65688e4d3d870516abbb3dba34436df44cd52/53cf119244fbdad6b04b8c9cd2d33090afeba06a/README.yaml @@ -44,9 +44,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 605 bioschema_properties: - name: Molecular dynamics trajectory of a POPG/SOD (50:50) bilayer at 310 K (Lipid17, GROMACS 2018.3, 100 ns) [NMRlipids simulation 605] + name: Molecular dynamics trajectory of a POPG/SOD (50:50) bilayer at 310 K (Lipid17, + GROMACS 2018.3, 100 ns) [NMRlipids simulation 605] alternateName: 500POPG_500SOD_25000SOL_310K - description: Molecular dynamics trajectory of a lipid bilayer of 500 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 50 mol%) and 500 SOD (50 mol%) at 310 K. Simulated with Lipid17 in GROMACS 2018.3 for 100 ns (139000 atoms). Deposited as NMRlipids Databank simulation 605 and available from https://doi.org/10.5281/zenodo.3832274. + description: Molecular dynamics trajectory of a lipid bilayer of 500 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, + 50 mol%) and 500 SOD (50 mol%) at 310 K. Simulated with Lipid17 in GROMACS 2018.3 + for 100 ns (139000 atoms). Deposited as NMRlipids Databank simulation 605 and + available from https://doi.org/10.5281/zenodo.3832274. sameAs: https://doi.org/10.5281/zenodo.3832274 datePublished: '2019-06-17' license: @@ -137,7 +141,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3832274 identifier: 10.5281/zenodo.3832274 url: https://doi.org/10.5281/zenodo.3832274 - name: LIPID17 POPG Bilayer Simulation (Last 100 ns, 310 K ) using dihedral type 9 + name: LIPID17 POPG Bilayer Simulation (Last 100 ns, 310 K ) using dihedral type + 9 publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/96f/656/96f65688e4d3d870516abbb3dba34436df44cd52/896f4f5def2afe1dc7bc98433a0d328f7cd8b38c/README.yaml b/Simulations/96f/656/96f65688e4d3d870516abbb3dba34436df44cd52/896f4f5def2afe1dc7bc98433a0d328f7cd8b38c/README.yaml index 69311fd459..54a8dcc7a0 100644 --- a/Simulations/96f/656/96f65688e4d3d870516abbb3dba34436df44cd52/896f4f5def2afe1dc7bc98433a0d328f7cd8b38c/README.yaml +++ b/Simulations/96f/656/96f65688e4d3d870516abbb3dba34436df44cd52/896f4f5def2afe1dc7bc98433a0d328f7cd8b38c/README.yaml @@ -45,9 +45,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 880 bioschema_properties: - name: Molecular dynamics trajectory of a POPG/SOD (50:50) bilayer at 310 K (Lipid17(1), GROMACS 5.1.3, 100 ns) [NMRlipids simulation 880] + name: Molecular dynamics trajectory of a POPG/SOD (50:50) bilayer at 310 K (Lipid17(1), + GROMACS 5.1.3, 100 ns) [NMRlipids simulation 880] alternateName: POPG:310K:Lipid17_specific_ver - description: Molecular dynamics trajectory of a lipid bilayer of 500 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 50 mol%) and 500 SOD (50 mol%) at 310 K. Simulated with Lipid17(1) in GROMACS 5.1.3 for 100 ns (139000 atoms). Deposited as NMRlipids Databank simulation 880 and available from https://doi.org/10.5281/zenodo.3832219. + description: Molecular dynamics trajectory of a lipid bilayer of 500 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, + 50 mol%) and 500 SOD (50 mol%) at 310 K. Simulated with Lipid17(1) in GROMACS + 5.1.3 for 100 ns (139000 atoms). Deposited as NMRlipids Databank simulation 880 + and available from https://doi.org/10.5281/zenodo.3832219. sameAs: https://doi.org/10.5281/zenodo.3832219 datePublished: '2020-05-18' license: @@ -140,7 +144,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3832219 identifier: 10.5281/zenodo.3832219 url: https://doi.org/10.5281/zenodo.3832219 - name: LIPID17 POPG Bilayer Simulation (Last 100ns, 310 K) using dihedral type 9 instead of type 1. + name: LIPID17 POPG Bilayer Simulation (Last 100ns, 310 K) using dihedral type + 9 instead of type 1. publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/977/24c/97724c50ee654fe3a562f4a4d375267c4412e378/edf885a67251116e28e418b9e96ce22bc9437bc3/README.yaml b/Simulations/977/24c/97724c50ee654fe3a562f4a4d375267c4412e378/edf885a67251116e28e418b9e96ce22bc9437bc3/README.yaml index 147f1b9abe..9710aa5e06 100644 --- a/Simulations/977/24c/97724c50ee654fe3a562f4a4d375267c4412e378/edf885a67251116e28e418b9e96ce22bc9437bc3/README.yaml +++ b/Simulations/977/24c/97724c50ee654fe3a562f4a4d375267c4412e378/edf885a67251116e28e418b9e96ce22bc9437bc3/README.yaml @@ -56,9 +56,14 @@ SOFTWARE: gromacs DIR_WRK: /usr/home/bort/Databank ID: 108 bioschema_properties: - name: Molecular dynamics trajectory of a DOPC/DAPC/CHOL (47:43:10) bilayer at 310 K (CHARMM36, GROMACS, 1000 ns) [NMRlipids simulation 108] + name: Molecular dynamics trajectory of a DOPC/DAPC/CHOL (47:43:10) bilayer at 310 + K (CHARMM36, GROMACS, 1000 ns) [NMRlipids simulation 108] alternateName: 28CHOL_130DOPC_120DAPC_11120SOL_310K - description: Molecular dynamics trajectory of a lipid bilayer of 130 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, 47 mol%), 120 DAPC (1,2-diarachidonoyl-sn-glycero-3-phosphocholine, 43 mol%) and 28 CHOL (cholesterol, 10 mol%) at 310 K. Simulated with CHARMM36 in GROMACS for 1000 ns (69932 atoms). Deposited as NMRlipids Databank simulation 108 and available from https://doi.org/10.5281/zenodo.2653723. + description: Molecular dynamics trajectory of a lipid bilayer of 130 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, + 47 mol%), 120 DAPC (1,2-diarachidonoyl-sn-glycero-3-phosphocholine, 43 mol%) and + 28 CHOL (cholesterol, 10 mol%) at 310 K. Simulated with CHARMM36 in GROMACS for + 1000 ns (69932 atoms). Deposited as NMRlipids Databank simulation 108 and available + from https://doi.org/10.5281/zenodo.2653723. sameAs: https://doi.org/10.5281/zenodo.2653723 datePublished: '2019-04-29' license: @@ -149,7 +154,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.2653723 identifier: 10.5281/zenodo.2653723 url: https://doi.org/10.5281/zenodo.2653723 - name: Atomistic simulations of cholesterol in asymmetric lipid bilayers with varying degrees of lipid chain unsaturation + name: Atomistic simulations of cholesterol in asymmetric lipid bilayers with varying + degrees of lipid chain unsaturation publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/978/ed7/978ed7ba7a6f4f1119b598f6d1084552fe34542f/fa3e0e4992a9099a0e3262451f820180f3f8b9d4/README.yaml b/Simulations/978/ed7/978ed7ba7a6f4f1119b598f6d1084552fe34542f/fa3e0e4992a9099a0e3262451f820180f3f8b9d4/README.yaml index 190d7e7e27..45a5eaffad 100644 --- a/Simulations/978/ed7/978ed7ba7a6f4f1119b598f6d1084552fe34542f/fa3e0e4992a9099a0e3262451f820180f3f8b9d4/README.yaml +++ b/Simulations/978/ed7/978ed7ba7a6f4f1119b598f6d1084552fe34542f/fa3e0e4992a9099a0e3262451f820180f3f8b9d4/README.yaml @@ -55,9 +55,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 176 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL/CHOL (43:31:16:11) bilayer at 310.15 K (CHARMM36, GROMACS 5.0, 2000 ns) [NMRlipids simulation 176] + name: Molecular dynamics trajectory of a POPC/CLA/CAL/CHOL (43:31:16:11) bilayer + at 310.15 K (CHARMM36, GROMACS 5.0, 2000 ns) [NMRlipids simulation 176] alternateName: 50CHOL_200POPC_9000SOL_73CAL_146CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 43 mol%), 146 CLA (31 mol%), 73 CAL (16 mol%) and 50 CHOL (cholesterol, 11 mol%) at 310.15 K. Simulated with CHARMM36 in GROMACS 5.0 for 2000 ns (57719 atoms). Deposited as NMRlipids Databank simulation 176 and available from https://doi.org/10.5281/zenodo.259365. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 43 mol%), 146 CLA (31 mol%), 73 CAL (16 mol%) and 50 CHOL (cholesterol, 11 mol%) + at 310.15 K. Simulated with CHARMM36 in GROMACS 5.0 for 2000 ns (57719 atoms). + Deposited as NMRlipids Databank simulation 176 and available from https://doi.org/10.5281/zenodo.259365. sameAs: https://doi.org/10.5281/zenodo.259365 datePublished: '2017-01-24' license: @@ -147,7 +151,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.259365 identifier: 10.5281/zenodo.259365 url: https://doi.org/10.5281/zenodo.259365 - name: Popc With Varying Amounts Of Cholesterol, 450 Mm Of Cacl_2. Charmm36 With Default Charmm Ions + name: Popc With Varying Amounts Of Cholesterol, 450 Mm Of Cacl_2. Charmm36 With + Default Charmm Ions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/98c/3c3/98c3c3506470ffd03f1f8f51882bc942fda776bc/7a498ed8f75ec51d5f5c61cef2f9aa214fa83af7/README.yaml b/Simulations/98c/3c3/98c3c3506470ffd03f1f8f51882bc942fda776bc/7a498ed8f75ec51d5f5c61cef2f9aa214fa83af7/README.yaml index c87ac43c8d..06ed8e8cd3 100644 --- a/Simulations/98c/3c3/98c3c3506470ffd03f1f8f51882bc942fda776bc/7a498ed8f75ec51d5f5c61cef2f9aa214fa83af7/README.yaml +++ b/Simulations/98c/3c3/98c3c3506470ffd03f1f8f51882bc942fda776bc/7a498ed8f75ec51d5f5c61cef2f9aa214fa83af7/README.yaml @@ -54,9 +54,13 @@ EXPERIMENT: CHOL: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a SDPE/CHOL/SDG (58:33:9) bilayer at 310 K (Lipid17, GROMACS 18.7, 1000 ns) [NMRlipids simulation 720] + name: Molecular dynamics trajectory of a SDPE/CHOL/SDG (58:33:9) bilayer at 310 + K (Lipid17, GROMACS 18.7, 1000 ns) [NMRlipids simulation 720] alternateName: DOGandCHOLinSDPEwithLipid17 - description: Molecular dynamics trajectory of a lipid bilayer of 74 SDPE (1-stearoyl-2-docosahexaenoyl-sn-glycero-3-phosphoethanolamine, 58 mol%), 42 CHOL (cholesterol, 33 mol%) and 12 SDG (1-stearoyl-2-docosahexaenoyl-sn-glycerol, 9 mol%) at 310 K. Simulated with Lipid17 in GROMACS 18.7 for 1000 ns (33590 atoms). Deposited as NMRlipids Databank simulation 720 and available from https://doi.org/10.5281/zenodo.6823140. + description: Molecular dynamics trajectory of a lipid bilayer of 74 SDPE (1-stearoyl-2-docosahexaenoyl-sn-glycero-3-phosphoethanolamine, + 58 mol%), 42 CHOL (cholesterol, 33 mol%) and 12 SDG (1-stearoyl-2-docosahexaenoyl-sn-glycerol, + 9 mol%) at 310 K. Simulated with Lipid17 in GROMACS 18.7 for 1000 ns (33590 atoms). + Deposited as NMRlipids Databank simulation 720 and available from https://doi.org/10.5281/zenodo.6823140. sameAs: https://doi.org/10.5281/zenodo.6823140 datePublished: '2022-07-12' license: diff --git a/Simulations/992/e7c/992e7cb56567854f229a3c45e0452a7bbb7a0ba7/d62a844544afff27fb2bc25fdcce9359a5717989/README.yaml b/Simulations/992/e7c/992e7cb56567854f229a3c45e0452a7bbb7a0ba7/d62a844544afff27fb2bc25fdcce9359a5717989/README.yaml index b8253d6d90..c8d6de5263 100644 --- a/Simulations/992/e7c/992e7cb56567854f229a3c45e0452a7bbb7a0ba7/d62a844544afff27fb2bc25fdcce9359a5717989/README.yaml +++ b/Simulations/992/e7c/992e7cb56567854f229a3c45e0452a7bbb7a0ba7/d62a844544afff27fb2bc25fdcce9359a5717989/README.yaml @@ -55,9 +55,14 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 197 bioschema_properties: - name: Molecular dynamics trajectory of a POPE/SOD/POPG/CLA (52:24:17:7) bilayer at 310 K (CHARMM36, GROMACS 5.1.2, 100 ns) [NMRlipids simulation 197] + name: Molecular dynamics trajectory of a POPE/SOD/POPG/CLA (52:24:17:7) bilayer + at 310 K (CHARMM36, GROMACS 5.1.2, 100 ns) [NMRlipids simulation 197] alternateName: 126POPG_374POPE_25000SOL_176SOD_50CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 374 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 52 mol%), 176 SOD (24 mol%), 126 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 17 mol%) and 50 CLA (7 mol%) at 310 K. Simulated with CHARMM36 in GROMACS 5.1.2 for 100 ns (137978 atoms). Deposited as NMRlipids Databank simulation 197 and available from https://doi.org/10.5281/zenodo.2579108. + description: Molecular dynamics trajectory of a lipid bilayer of 374 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, + 52 mol%), 176 SOD (24 mol%), 126 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, + 17 mol%) and 50 CLA (7 mol%) at 310 K. Simulated with CHARMM36 in GROMACS 5.1.2 + for 100 ns (137978 atoms). Deposited as NMRlipids Databank simulation 197 and + available from https://doi.org/10.5281/zenodo.2579108. sameAs: https://doi.org/10.5281/zenodo.2579108 datePublished: '2019-02-27' license: @@ -150,7 +155,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.2579108 identifier: 10.5281/zenodo.2579108 url: https://doi.org/10.5281/zenodo.2579108 - name: CHARMM36 POPG-POPE 1:3 Bilayer Simulation (Last 100 ns, 150 mM NaCl, 310 K ) + name: CHARMM36 POPG-POPE 1:3 Bilayer Simulation (Last 100 ns, 150 mM NaCl, 310 + K ) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/995/877/9958771b8fb92ac07be7d4285d09f8df65cc758e/5ad07cc3a737f917dc0e69d6f00b44091322ff68/README.yaml b/Simulations/995/877/9958771b8fb92ac07be7d4285d09f8df65cc758e/5ad07cc3a737f917dc0e69d6f00b44091322ff68/README.yaml index f451fd7c0d..18902ad8b0 100644 --- a/Simulations/995/877/9958771b8fb92ac07be7d4285d09f8df65cc758e/5ad07cc3a737f917dc0e69d6f00b44091322ff68/README.yaml +++ b/Simulations/995/877/9958771b8fb92ac07be7d4285d09f8df65cc758e/5ad07cc3a737f917dc0e69d6f00b44091322ff68/README.yaml @@ -47,9 +47,12 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/1 ID: 573 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 300 K (ECC-lipids, GROMACS 5.1.4, 300 ns) [NMRlipids simulation 573] + name: Molecular dynamics trajectory of a POPC bilayer at 300 K (ECC-lipids, GROMACS + 5.1.4, 300 ns) [NMRlipids simulation 573] alternateName: 128POPC_6400SOL_300K - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 300 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 300 ns (36352 atoms). Deposited as NMRlipids Databank simulation 573 and available from https://doi.org/10.5281/zenodo.3335503. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 300 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 300 ns (36352 atoms). + Deposited as NMRlipids Databank simulation 573 and available from https://doi.org/10.5281/zenodo.3335503. sameAs: https://doi.org/10.5281/zenodo.3335503 datePublished: '2017-12-19' license: @@ -143,7 +146,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3335503 identifier: 10.5281/zenodo.3335503 url: https://doi.org/10.5281/zenodo.3335503 - name: Simulations of POPC lipid bilayer in water solution at various NaCl, KCl and CaCl2 concentrations using ECC-POPC force field + name: Simulations of POPC lipid bilayer in water solution at various NaCl, KCl + and CaCl2 concentrations using ECC-POPC force field publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/999/60d/99960db731abc24358eea3b5edf4eaff335c1ba3/cdf412c4bd1e99664ba8d0995e5490480942938c/README.yaml b/Simulations/999/60d/99960db731abc24358eea3b5edf4eaff335c1ba3/cdf412c4bd1e99664ba8d0995e5490480942938c/README.yaml index 3b2ff3ca59..d6db271003 100644 --- a/Simulations/999/60d/99960db731abc24358eea3b5edf4eaff335c1ba3/cdf412c4bd1e99664ba8d0995e5490480942938c/README.yaml +++ b/Simulations/999/60d/99960db731abc24358eea3b5edf4eaff335c1ba3/cdf412c4bd1e99664ba8d0995e5490480942938c/README.yaml @@ -48,9 +48,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 249 bioschema_properties: - name: Molecular dynamics trajectory of a CHOL/POPC (50:50) bilayer at 310 K (Slipids, GROMACS 4.6, 500 ns) [NMRlipids simulation 249] + name: Molecular dynamics trajectory of a CHOL/POPC (50:50) bilayer at 310 K (Slipids, + GROMACS 4.6, 500 ns) [NMRlipids simulation 249] alternateName: 200POPC_9000SOL_200CHOL_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 CHOL (cholesterol, 50 mol%) and 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 50 mol%) at 310 K. Simulated with Slipids in GROMACS 4.6 for 500 ns (95600 atoms). Deposited as NMRlipids Databank simulation 249 and available from https://doi.org/10.5281/zenodo.3243329. + description: Molecular dynamics trajectory of a lipid bilayer of 200 CHOL (cholesterol, + 50 mol%) and 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 50 mol%) + at 310 K. Simulated with Slipids in GROMACS 4.6 for 500 ns (95600 atoms). Deposited + as NMRlipids Databank simulation 249 and available from https://doi.org/10.5281/zenodo.3243329. sameAs: https://doi.org/10.5281/zenodo.3243329 datePublished: '2016-09-18' license: diff --git a/Simulations/9a1/605/9a16054f3de88c6236c869a48b7ba22a4560c031/1ee911c0a7597ddccc6a2f88e6de0103731df881/README.yaml b/Simulations/9a1/605/9a16054f3de88c6236c869a48b7ba22a4560c031/1ee911c0a7597ddccc6a2f88e6de0103731df881/README.yaml index 748794d6fb..5331aa53dc 100644 --- a/Simulations/9a1/605/9a16054f3de88c6236c869a48b7ba22a4560c031/1ee911c0a7597ddccc6a2f88e6de0103731df881/README.yaml +++ b/Simulations/9a1/605/9a16054f3de88c6236c869a48b7ba22a4560c031/1ee911c0a7597ddccc6a2f88e6de0103731df881/README.yaml @@ -54,9 +54,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 15 bioschema_properties: - name: Molecular dynamics trajectory of a CHOL/POPC (61:39) bilayer at 298 K (Berger and Modified Höltje model for cholesterol, GROMACS 4.5, 50 ns) [NMRlipids simulation 15] + name: Molecular dynamics trajectory of a CHOL/POPC (61:39) bilayer at 298 K (Berger + and Modified Höltje model for cholesterol, GROMACS 4.5, 50 ns) [NMRlipids simulation + 15] alternateName: 78CHOL_50POPC_5782SOL_298K_Berger - description: Molecular dynamics trajectory of a lipid bilayer of 78 CHOL (cholesterol, 61 mol%) and 50 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 39 mol%) at 298 K. Simulated with Berger and Modified Höltje model for cholesterol in GROMACS 4.5 for 50 ns (22208 atoms). Deposited as NMRlipids Databank simulation 15 and available from https://doi.org/10.5281/zenodo.4644028. + description: Molecular dynamics trajectory of a lipid bilayer of 78 CHOL (cholesterol, + 61 mol%) and 50 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 39 mol%) + at 298 K. Simulated with Berger and Modified Höltje model for cholesterol in GROMACS + 4.5 for 50 ns (22208 atoms). Deposited as NMRlipids Databank simulation 15 and + available from https://doi.org/10.5281/zenodo.4644028. sameAs: https://doi.org/10.5281/zenodo.4644028 datePublished: '2014-12-17' license: @@ -151,7 +157,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.4644028 identifier: 10.5281/zenodo.4644028 url: https://doi.org/10.5281/zenodo.4644028 - name: MD simulation trajectory and related files for POPC/cholesterol (60 mol%) bilayer (Berger model delivered by Tieleman, modified Höltje, Gromacs 4.5) + name: MD simulation trajectory and related files for POPC/cholesterol (60 mol%) + bilayer (Berger model delivered by Tieleman, modified Höltje, Gromacs 4.5) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/9a7/003/9a700315b567dea72fe8509c0d33481ba2a49075/a4e20018c3970fd47f3fb93ac5be709892261c09/README.yaml b/Simulations/9a7/003/9a700315b567dea72fe8509c0d33481ba2a49075/a4e20018c3970fd47f3fb93ac5be709892261c09/README.yaml index aa90098ce8..2fc65a1eea 100644 --- a/Simulations/9a7/003/9a700315b567dea72fe8509c0d33481ba2a49075/a4e20018c3970fd47f3fb93ac5be709892261c09/README.yaml +++ b/Simulations/9a7/003/9a700315b567dea72fe8509c0d33481ba2a49075/a4e20018c3970fd47f3fb93ac5be709892261c09/README.yaml @@ -47,9 +47,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 293 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (73:14:14) bilayer at 298 K (MacRog, GROMACS 4.5, 50 ns) [NMRlipids simulation 293] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (73:14:14) bilayer at 298 + K (MacRog, GROMACS 4.5, 50 ns) [NMRlipids simulation 293] alternateName: 288POPC_14500SOL_54SOD_54CLA_298K - description: Molecular dynamics trajectory of a lipid bilayer of 288 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 73 mol%), 54 CLA (14 mol%) and 54 SOD (14 mol%) at 298 K. Simulated with MacRog in GROMACS 4.5 for 50 ns (82200 atoms). Deposited as NMRlipids Databank simulation 293 and available from https://doi.org/10.5281/zenodo.14976. + description: Molecular dynamics trajectory of a lipid bilayer of 288 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 73 mol%), 54 CLA (14 mol%) and 54 SOD (14 mol%) at 298 K. Simulated with MacRog + in GROMACS 4.5 for 50 ns (82200 atoms). Deposited as NMRlipids Databank simulation + 293 and available from https://doi.org/10.5281/zenodo.14976. sameAs: https://doi.org/10.5281/zenodo.14976 datePublished: '2015-02-10' license: diff --git a/Simulations/9a8/b91/9a8b913b3ef4edd0590ee766bf95ef122b4cc8f5/189ac1c9fab4ddc8a1fd9a2d174e84dbd7d5323a/README.yaml b/Simulations/9a8/b91/9a8b913b3ef4edd0590ee766bf95ef122b4cc8f5/189ac1c9fab4ddc8a1fd9a2d174e84dbd7d5323a/README.yaml index 57371bbacb..f0e974442b 100644 --- a/Simulations/9a8/b91/9a8b913b3ef4edd0590ee766bf95ef122b4cc8f5/189ac1c9fab4ddc8a1fd9a2d174e84dbd7d5323a/README.yaml +++ b/Simulations/9a8/b91/9a8b913b3ef4edd0590ee766bf95ef122b4cc8f5/189ac1c9fab4ddc8a1fd9a2d174e84dbd7d5323a/README.yaml @@ -43,9 +43,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 404 bioschema_properties: - name: Molecular dynamics trajectory of a DPPG/SOD (50:50) bilayer at 314 K (Slipids, GROMACS 5.0.4, 50 ns) [NMRlipids simulation 404] + name: Molecular dynamics trajectory of a DPPG/SOD (50:50) bilayer at 314 K (Slipids, + GROMACS 5.0.4, 50 ns) [NMRlipids simulation 404] alternateName: 288DPPG_11232SOL_288SOD_314K - description: Molecular dynamics trajectory of a lipid bilayer of 288 DPPG (1,2-dipalmitoyl-sn-glycero-3-phospho-(1’-rac-glycerol), 50 mol%) and 288 SOD (50 mol%) at 314 K. Simulated with Slipids in GROMACS 5.0.4 for 50 ns (69408 atoms). Deposited as NMRlipids Databank simulation 404 and available from https://doi.org/10.5281/zenodo.546136. + description: Molecular dynamics trajectory of a lipid bilayer of 288 DPPG (1,2-dipalmitoyl-sn-glycero-3-phospho-(1’-rac-glycerol), + 50 mol%) and 288 SOD (50 mol%) at 314 K. Simulated with Slipids in GROMACS 5.0.4 + for 50 ns (69408 atoms). Deposited as NMRlipids Databank simulation 404 and available + from https://doi.org/10.5281/zenodo.546136. sameAs: https://doi.org/10.5281/zenodo.546136 datePublished: '2017-04-13' license: @@ -133,7 +137,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.546136 identifier: 10.5281/zenodo.546136 url: https://doi.org/10.5281/zenodo.546136 - name: 'Md Simulation Trajectory Of A Fully Hydrated Dppg Bilayer @314K: Slipids, Gromacs 5.0.4. 2017.' + name: 'Md Simulation Trajectory Of A Fully Hydrated Dppg Bilayer @314K: Slipids, + Gromacs 5.0.4. 2017.' publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/9af/4b3/9af4b30744b173720527d8993ee2a21fafa22180/97864d343fe0cd410d5f746fb6f6f3ed453d21fd/README.yaml b/Simulations/9af/4b3/9af4b30744b173720527d8993ee2a21fafa22180/97864d343fe0cd410d5f746fb6f6f3ed453d21fd/README.yaml index c80f9804b5..b2050d4ea4 100644 --- a/Simulations/9af/4b3/9af4b30744b173720527d8993ee2a21fafa22180/97864d343fe0cd410d5f746fb6f6f3ed453d21fd/README.yaml +++ b/Simulations/9af/4b3/9af4b30744b173720527d8993ee2a21fafa22180/97864d343fe0cd410d5f746fb6f6f3ed453d21fd/README.yaml @@ -43,9 +43,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 126 bioschema_properties: - name: Molecular dynamics trajectory of a DPPE bilayer at 342 K (GROMOS-CKP, GROMACS 5.0.6, 400 ns) [NMRlipids simulation 126] + name: Molecular dynamics trajectory of a DPPE bilayer at 342 K (GROMOS-CKP, GROMACS + 5.0.6, 400 ns) [NMRlipids simulation 126] alternateName: 128DPPE_3655SOL_342K_GROMOS-CKP_v1 - description: Molecular dynamics trajectory of a lipid bilayer of 128 DPPE (1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine) at 342 K. Simulated with GROMOS-CKP in GROMACS 5.0.6 for 400 ns (17365 atoms). Deposited as NMRlipids Databank simulation 126 and available from https://doi.org/10.5281/zenodo.1293957. + description: Molecular dynamics trajectory of a lipid bilayer of 128 DPPE (1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine) + at 342 K. Simulated with GROMOS-CKP in GROMACS 5.0.6 for 400 ns (17365 atoms). + Deposited as NMRlipids Databank simulation 126 and available from https://doi.org/10.5281/zenodo.1293957. sameAs: https://doi.org/10.5281/zenodo.1293957 datePublished: '2018-06-20' license: diff --git a/Simulations/9b3/085/9b3085df71a90fb15bde7f9152d811fc1b1ad346/79a426c93cd61c106a63f07bd053a1ac0c526ddd/README.yaml b/Simulations/9b3/085/9b3085df71a90fb15bde7f9152d811fc1b1ad346/79a426c93cd61c106a63f07bd053a1ac0c526ddd/README.yaml index 4ee7b8e331..07980b6f85 100644 --- a/Simulations/9b3/085/9b3085df71a90fb15bde7f9152d811fc1b1ad346/79a426c93cd61c106a63f07bd053a1ac0c526ddd/README.yaml +++ b/Simulations/9b3/085/9b3085df71a90fb15bde7f9152d811fc1b1ad346/79a426c93cd61c106a63f07bd053a1ac0c526ddd/README.yaml @@ -49,9 +49,13 @@ CPT: null DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 321 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (55:30:15) bilayer at 303 K (CHARMM36, GROMACS 5.0.4, 100 ns) [NMRlipids simulation 321] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (55:30:15) bilayer at 303 + K (CHARMM36, GROMACS 5.0.4, 100 ns) [NMRlipids simulation 321] alternateName: POPC_CHARMM36_CaCl2_035Mol_303K - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 55 mol%), 70 CLA (30 mol%) and 35 CAL (15 mol%) at 303 K. Simulated with CHARMM36 in GROMACS 5.0.4 for 100 ns (36457 atoms). Deposited as NMRlipids Databank simulation 321 and available from https://doi.org/10.5281/zenodo.35159. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 55 mol%), 70 CLA (30 mol%) and 35 CAL (15 mol%) at 303 K. Simulated with CHARMM36 + in GROMACS 5.0.4 for 100 ns (36457 atoms). Deposited as NMRlipids Databank simulation + 321 and available from https://doi.org/10.5281/zenodo.35159. sameAs: https://doi.org/10.5281/zenodo.35159 datePublished: '2015-12-10' license: diff --git a/Simulations/9b7/641/9b764160ba3d106354f828531981eef8b34e8306/262e4fd83c0f60c7de432db3961400e314457a12/README.yaml b/Simulations/9b7/641/9b764160ba3d106354f828531981eef8b34e8306/262e4fd83c0f60c7de432db3961400e314457a12/README.yaml index 444d9a7961..511b05a9bf 100644 --- a/Simulations/9b7/641/9b764160ba3d106354f828531981eef8b34e8306/262e4fd83c0f60c7de432db3961400e314457a12/README.yaml +++ b/Simulations/9b7/641/9b764160ba3d106354f828531981eef8b34e8306/262e4fd83c0f60c7de432db3961400e314457a12/README.yaml @@ -56,9 +56,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 371 bioschema_properties: - name: Molecular dynamics trajectory of a CLA/DHMDMAB/POPC (33:33:33) bilayer at 313 K (ECC-lipids, GROMACS 5.1.4, 200 ns) [NMRlipids simulation 371] + name: Molecular dynamics trajectory of a CLA/DHMDMAB/POPC (33:33:33) bilayer at + 313 K (ECC-lipids, GROMACS 5.1.4, 200 ns) [NMRlipids simulation 371] alternateName: 100POPC_6214SOL_100DHMDMAB_100CLA_313K_SPCEmodel - description: Molecular dynamics trajectory of a lipid bilayer of 100 CLA (33 mol%), 100 DHMDMAB (dihexadecyldimethylammonium, 33 mol%) and 100 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 33 mol%) at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 200 ns (42842 atoms). Deposited as NMRlipids Databank simulation 371 and available from https://doi.org/10.5281/zenodo.1118682. + description: Molecular dynamics trajectory of a lipid bilayer of 100 CLA (33 mol%), + 100 DHMDMAB (dihexadecyldimethylammonium, 33 mol%) and 100 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 33 mol%) at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 200 ns (42842 + atoms). Deposited as NMRlipids Databank simulation 371 and available from https://doi.org/10.5281/zenodo.1118682. sameAs: https://doi.org/10.5281/zenodo.1118682 datePublished: '2017-12-19' license: @@ -149,7 +153,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1118682 identifier: 10.5281/zenodo.1118682 url: https://doi.org/10.5281/zenodo.1118682 - name: Simulations Of Popc Lipid Bilayer In Water Solution With Various Molar Fractions Of Cationic Surfactant Dihexadecylammonium Using Ecc-Popc Force Field + name: Simulations Of Popc Lipid Bilayer In Water Solution With Various Molar Fractions + Of Cationic Surfactant Dihexadecylammonium Using Ecc-Popc Force Field publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/9cc/a43/9cca43b014e94e814ad67fa24422986dd1effb72/93cad0b1b10eb15dc60d41489a6821f40ee4cb69/README.yaml b/Simulations/9cc/a43/9cca43b014e94e814ad67fa24422986dd1effb72/93cad0b1b10eb15dc60d41489a6821f40ee4cb69/README.yaml index 07f121c45d..63170dc345 100644 --- a/Simulations/9cc/a43/9cca43b014e94e814ad67fa24422986dd1effb72/93cad0b1b10eb15dc60d41489a6821f40ee4cb69/README.yaml +++ b/Simulations/9cc/a43/9cca43b014e94e814ad67fa24422986dd1effb72/93cad0b1b10eb15dc60d41489a6821f40ee4cb69/README.yaml @@ -39,9 +39,13 @@ DATEOFRUNNING: '2026-09-16' TYPEOFSYSTEM: lipid bilayer ID: 938 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC bilayer at 326 K (prosECCo 75 paper related data, GROMACS 2022.5-plumed_2.8.2, 1000 ns) [NMRlipids simulation -1] + name: Molecular dynamics trajectory of a DPPC bilayer at 326 K (prosECCo 75 paper + related data, GROMACS 2022.5-plumed_2.8.2, 1000 ns) [NMRlipids simulation -1] alternateName: DPPC_200_SOL_9000_prosECCo75_LO_326K - description: Molecular dynamics trajectory of a lipid bilayer of 200 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) at 326 K. Simulated with prosECCo 75 paper related data in GROMACS 2022.5-plumed_2.8.2 for 1000 ns (53000 atoms). Deposited as NMRlipids Databank simulation -1 and available from https://doi.org/10.5281/zenodo.10635500. + description: Molecular dynamics trajectory of a lipid bilayer of 200 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) + at 326 K. Simulated with prosECCo 75 paper related data in GROMACS 2022.5-plumed_2.8.2 + for 1000 ns (53000 atoms). Deposited as NMRlipids Databank simulation -1 and available + from https://doi.org/10.5281/zenodo.10635500. sameAs: https://doi.org/10.5281/zenodo.10635500 datePublished: '2024-02-08' license: @@ -137,3 +141,7 @@ bioschema_properties: doi: 10.5281/zenodo.10635500 spdxLicenseList: 3.29.0 retrieved: '2026-09-22' +EXPERIMENT: + ORDERPARAMETER: + DPPC: [] + FORMFACTOR: [] diff --git a/Simulations/9d1/f02/9d1f02cbebbcdb0b8e5c0c9e3b91cf98eda37c14/f41ddc0cdb7cead26ba01370fde3af901f0509c7/README.yaml b/Simulations/9d1/f02/9d1f02cbebbcdb0b8e5c0c9e3b91cf98eda37c14/f41ddc0cdb7cead26ba01370fde3af901f0509c7/README.yaml index b620f89584..abba3174cf 100644 --- a/Simulations/9d1/f02/9d1f02cbebbcdb0b8e5c0c9e3b91cf98eda37c14/f41ddc0cdb7cead26ba01370fde3af901f0509c7/README.yaml +++ b/Simulations/9d1/f02/9d1f02cbebbcdb0b8e5c0c9e3b91cf98eda37c14/f41ddc0cdb7cead26ba01370fde3af901f0509c7/README.yaml @@ -57,9 +57,14 @@ EXPERIMENT: TLCL_0H: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POT/TLCL_0H/CLA (48:32:12:8) bilayer at 303.15 K (CHARMM36, GROMACS 5.0.6, 500 ns) [NMRlipids simulation 779] + name: Molecular dynamics trajectory of a POPC/POT/TLCL_0H/CLA (48:32:12:8) bilayer + at 303.15 K (CHARMM36, GROMACS 5.0.6, 500 ns) [NMRlipids simulation 779] alternateName: TLCL:POPC(30%)50mM-CHARMM - description: Molecular dynamics trajectory of a lipid bilayer of 80 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 48 mol%), 54 POT (32 mol%), 20 TLCL_0H (tetralinoleoyl cardiolipin(2−), 12 mol%) and 14 CLA (8 mol%) at 303.15 K. Simulated with CHARMM36 in GROMACS 5.0.6 for 500 ns (60987 atoms). Deposited as NMRlipids Databank simulation 779 and available from https://doi.org/10.5281/zenodo.8386813. + description: Molecular dynamics trajectory of a lipid bilayer of 80 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 48 mol%), 54 POT (32 mol%), 20 TLCL_0H (tetralinoleoyl cardiolipin(2−), 12 mol%) + and 14 CLA (8 mol%) at 303.15 K. Simulated with CHARMM36 in GROMACS 5.0.6 for + 500 ns (60987 atoms). Deposited as NMRlipids Databank simulation 779 and available + from https://doi.org/10.5281/zenodo.8386813. sameAs: https://doi.org/10.5281/zenodo.8386813 datePublished: '2023-09-28' license: diff --git a/Simulations/9d2/67f/9d267f56ef99de1cb49df40a6da0c1da899b1ec8/fccd67de4e74b6b5fe026898b32d34bbeca2fb81/README.yaml b/Simulations/9d2/67f/9d267f56ef99de1cb49df40a6da0c1da899b1ec8/fccd67de4e74b6b5fe026898b32d34bbeca2fb81/README.yaml index 9cfda301ca..393db2907c 100644 --- a/Simulations/9d2/67f/9d267f56ef99de1cb49df40a6da0c1da899b1ec8/fccd67de4e74b6b5fe026898b32d34bbeca2fb81/README.yaml +++ b/Simulations/9d2/67f/9d267f56ef99de1cb49df40a6da0c1da899b1ec8/fccd67de4e74b6b5fe026898b32d34bbeca2fb81/README.yaml @@ -49,9 +49,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 609 bioschema_properties: - name: Molecular dynamics trajectory of a DAPC/CHOL (90:10) bilayer at 298 K (CHARMM36, GROMACS, 2000 ns) [NMRlipids simulation 609] + name: Molecular dynamics trajectory of a DAPC/CHOL (90:10) bilayer at 298 K (CHARMM36, + GROMACS, 2000 ns) [NMRlipids simulation 609] alternateName: 260DAPC_28CHOL_11520SOL_298K - description: Molecular dynamics trajectory of a lipid bilayer of 260 DAPC (1,2-diarachidonoyl-sn-glycero-3-phosphocholine, 90 mol%) and 28 CHOL (cholesterol, 10 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for 2000 ns (72512 atoms). Deposited as NMRlipids Databank simulation 609 and available from https://doi.org/10.5281/zenodo.2653735. + description: Molecular dynamics trajectory of a lipid bilayer of 260 DAPC (1,2-diarachidonoyl-sn-glycero-3-phosphocholine, + 90 mol%) and 28 CHOL (cholesterol, 10 mol%) at 298 K. Simulated with CHARMM36 + in GROMACS for 2000 ns (72512 atoms). Deposited as NMRlipids Databank simulation + 609 and available from https://doi.org/10.5281/zenodo.2653735. sameAs: https://doi.org/10.5281/zenodo.2653735 datePublished: '2019-04-29' license: @@ -140,7 +144,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.2653735 identifier: 10.5281/zenodo.2653735 url: https://doi.org/10.5281/zenodo.2653735 - name: Atomistic simulations of DAPC/cholesterol bilayers with one cholesterol restrained to the membrane core + name: Atomistic simulations of DAPC/cholesterol bilayers with one cholesterol + restrained to the membrane core publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/9d4/8ee/9d48ee2b39db6c4f2804c02bdb9747af1b426c91/5a7740d3bffebc76b167f75c47563a642294c48f/README.yaml b/Simulations/9d4/8ee/9d48ee2b39db6c4f2804c02bdb9747af1b426c91/5a7740d3bffebc76b167f75c47563a642294c48f/README.yaml index c50bfcb28c..0349be6e18 100644 --- a/Simulations/9d4/8ee/9d48ee2b39db6c4f2804c02bdb9747af1b426c91/5a7740d3bffebc76b167f75c47563a642294c48f/README.yaml +++ b/Simulations/9d4/8ee/9d48ee2b39db6c4f2804c02bdb9747af1b426c91/5a7740d3bffebc76b167f75c47563a642294c48f/README.yaml @@ -55,9 +55,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 265 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/SOD/POPG/CLA (47:27:20:6) bilayer at 310 K (Slipids, GROMACS 5.1.2, 100 ns) [NMRlipids simulation 265] + name: Molecular dynamics trajectory of a POPC/SOD/POPG/CLA (47:27:20:6) bilayer + at 310 K (Slipids, GROMACS 5.1.2, 100 ns) [NMRlipids simulation 265] alternateName: 150POPG_350POPC_25000SOL_198SOD_48CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 350 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 47 mol%), 198 SOD (27 mol%), 150 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 20 mol%) and 48 CLA (6 mol%) at 310 K. Simulated with Slipids in GROMACS 5.1.2 for 100 ns (141196 atoms). Deposited as NMRlipids Databank simulation 265 and available from https://doi.org/10.5281/zenodo.2581186. + description: Molecular dynamics trajectory of a lipid bilayer of 350 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 47 mol%), 198 SOD (27 mol%), 150 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, + 20 mol%) and 48 CLA (6 mol%) at 310 K. Simulated with Slipids in GROMACS 5.1.2 + for 100 ns (141196 atoms). Deposited as NMRlipids Databank simulation 265 and + available from https://doi.org/10.5281/zenodo.2581186. sameAs: https://doi.org/10.5281/zenodo.2581186 datePublished: '2019-03-03' license: @@ -147,7 +152,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.2581186 identifier: 10.5281/zenodo.2581186 url: https://doi.org/10.5281/zenodo.2581186 - name: SLIPID POPC-POPG 7:3 Bilayer Simulation (Last 100 ns, 150 mM NaCl, 310 K ) + name: SLIPID POPC-POPG 7:3 Bilayer Simulation (Last 100 ns, 150 mM NaCl, 310 K + ) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/9da/554/9da554e9ba7fc98d12d7bebfcc0e9defe3617bd7/9da554e9ba7fc98d12d7bebfcc0e9defe3617bd7/README.yaml b/Simulations/9da/554/9da554e9ba7fc98d12d7bebfcc0e9defe3617bd7/9da554e9ba7fc98d12d7bebfcc0e9defe3617bd7/README.yaml index 0a2e590d48..d66b1d870c 100644 --- a/Simulations/9da/554/9da554e9ba7fc98d12d7bebfcc0e9defe3617bd7/9da554e9ba7fc98d12d7bebfcc0e9defe3617bd7/README.yaml +++ b/Simulations/9da/554/9da554e9ba7fc98d12d7bebfcc0e9defe3617bd7/9da554e9ba7fc98d12d7bebfcc0e9defe3617bd7/README.yaml @@ -39,9 +39,12 @@ EXPERIMENT: DLIPC: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a DLIPC bilayer at 298 K (Charmm36, NAMD, 1 ns) [NMRlipids simulation 775] + name: Molecular dynamics trajectory of a DLIPC bilayer at 298 K (Charmm36, NAMD, + 1 ns) [NMRlipids simulation 775] alternateName: DLIPC simulation - description: Molecular dynamics trajectory of a lipid bilayer of 200 DLIPC (1,2-dilinoleoyl-sn-glycero-3-phosphocholine) at 298 K. Simulated with Charmm36 in NAMD for 1 ns (53800 atoms). Deposited as NMRlipids Databank simulation 775 and available from https://doi.org/10.5281/zenodo.8357170. + description: Molecular dynamics trajectory of a lipid bilayer of 200 DLIPC (1,2-dilinoleoyl-sn-glycero-3-phosphocholine) + at 298 K. Simulated with Charmm36 in NAMD for 1 ns (53800 atoms). Deposited as + NMRlipids Databank simulation 775 and available from https://doi.org/10.5281/zenodo.8357170. sameAs: https://doi.org/10.5281/zenodo.8357170 datePublished: '2023-09-18' license: diff --git a/Simulations/9db/dcf/9dbdcf57566ff21b7d921a0f7e4b155396f2642e/cf96fcc717fd7b8fc9b7c7ee70faf4d337b6c1f2/README.yaml b/Simulations/9db/dcf/9dbdcf57566ff21b7d921a0f7e4b155396f2642e/cf96fcc717fd7b8fc9b7c7ee70faf4d337b6c1f2/README.yaml index 113503c935..5109022673 100644 --- a/Simulations/9db/dcf/9dbdcf57566ff21b7d921a0f7e4b155396f2642e/cf96fcc717fd7b8fc9b7c7ee70faf4d337b6c1f2/README.yaml +++ b/Simulations/9db/dcf/9dbdcf57566ff21b7d921a0f7e4b155396f2642e/cf96fcc717fd7b8fc9b7c7ee70faf4d337b6c1f2/README.yaml @@ -52,9 +52,13 @@ EXPERIMENT: TLCL_0H: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a SOD/TLCL_0H/CLA (64:29:7) bilayer at 303.15 K (Charmm36, GROMACS 2023.2, 500 ns) [NMRlipids simulation 825] + name: Molecular dynamics trajectory of a SOD/TLCL_0H/CLA (64:29:7) bilayer at 303.15 + K (Charmm36, GROMACS 2023.2, 500 ns) [NMRlipids simulation 825] alternateName: TLCL_66_Na_Cl_T303_45w/P - description: Molecular dynamics trajectory of a lipid bilayer of 147 SOD (64 mol%), 66 TLCL_0H (tetralinoleoyl cardiolipin(2−), 29 mol%) and 15 CLA (7 mol%) at 303.15 K. Simulated with Charmm36 in GROMACS 2023.2 for 500 ns (33933 atoms). Deposited as NMRlipids Databank simulation 825 and available from https://doi.org/10.5281/zenodo.13933145. + description: Molecular dynamics trajectory of a lipid bilayer of 147 SOD (64 mol%), + 66 TLCL_0H (tetralinoleoyl cardiolipin(2−), 29 mol%) and 15 CLA (7 mol%) at 303.15 + K. Simulated with Charmm36 in GROMACS 2023.2 for 500 ns (33933 atoms). Deposited + as NMRlipids Databank simulation 825 and available from https://doi.org/10.5281/zenodo.13933145. sameAs: https://doi.org/10.5281/zenodo.13933145 datePublished: '2024-10-15' license: diff --git a/Simulations/9e5/d4e/9e5d4ec35e04867608e230e2425b609d3c26654b/fd5c1bd3057280a314e4d16762b768cfd683ff29/README.yaml b/Simulations/9e5/d4e/9e5d4ec35e04867608e230e2425b609d3c26654b/fd5c1bd3057280a314e4d16762b768cfd683ff29/README.yaml index 87f8d88154..d061c91d64 100644 --- a/Simulations/9e5/d4e/9e5d4ec35e04867608e230e2425b609d3c26654b/fd5c1bd3057280a314e4d16762b768cfd683ff29/README.yaml +++ b/Simulations/9e5/d4e/9e5d4ec35e04867608e230e2425b609d3c26654b/fd5c1bd3057280a314e4d16762b768cfd683ff29/README.yaml @@ -57,9 +57,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 354 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/PAzePCdeprot/POT (54:23:23) bilayer at 298 K (Berger, GROMACS 4.5, 60 ns) [NMRlipids simulation 354] + name: Molecular dynamics trajectory of a POPC/PAzePCdeprot/POT (54:23:23) bilayer + at 298 K (Berger, GROMACS 4.5, 60 ns) [NMRlipids simulation 354] alternateName: 90POPC_38PAzePCdeprot_7250SOL_38POT_298K - description: Molecular dynamics trajectory of a lipid bilayer of 90 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 54 mol%), 38 PAzePCdeprot (1-palmitoyl-2-azelaoyl-sn-glycero-3-phosphocholine deprotonated, 23 mol%) and 38 POT (23 mol%) at 298 K. Simulated with Berger in GROMACS 4.5 for 60 ns (28178 atoms). Deposited as NMRlipids Databank simulation 354 and available from https://doi.org/10.5281/zenodo.44622. + description: Molecular dynamics trajectory of a lipid bilayer of 90 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 54 mol%), 38 PAzePCdeprot (1-palmitoyl-2-azelaoyl-sn-glycero-3-phosphocholine + deprotonated, 23 mol%) and 38 POT (23 mol%) at 298 K. Simulated with Berger in + GROMACS 4.5 for 60 ns (28178 atoms). Deposited as NMRlipids Databank simulation + 354 and available from https://doi.org/10.5281/zenodo.44622. sameAs: https://doi.org/10.5281/zenodo.44622 datePublished: '2016-01-12' license: @@ -152,7 +157,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.44622 identifier: 10.5281/zenodo.44622 url: https://doi.org/10.5281/zenodo.44622 - name: MD simulation trajectory and related files for POPC bilayer with 30 mol% of deprotonated pazePC (Berger, Gromacs 4.5.) + name: MD simulation trajectory and related files for POPC bilayer with 30 mol% + of deprotonated pazePC (Berger, Gromacs 4.5.) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/9e6/063/9e60635b4cc2ab8156bafab587497006e5c27830/27e04320d664bc2bde5131c4d195fef3a29a1d3a/README.yaml b/Simulations/9e6/063/9e60635b4cc2ab8156bafab587497006e5c27830/27e04320d664bc2bde5131c4d195fef3a29a1d3a/README.yaml index 72dea0dd41..2b97a45ddc 100644 --- a/Simulations/9e6/063/9e60635b4cc2ab8156bafab587497006e5c27830/27e04320d664bc2bde5131c4d195fef3a29a1d3a/README.yaml +++ b/Simulations/9e6/063/9e60635b4cc2ab8156bafab587497006e5c27830/27e04320d664bc2bde5131c4d195fef3a29a1d3a/README.yaml @@ -50,9 +50,13 @@ EXPERIMENT: CHOL: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a DOPC/CHOL (53:47) bilayer at 333.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 643] + name: Molecular dynamics trajectory of a DOPC/CHOL (53:47) bilayer at 333.15 K (CHARMM36, + GROMACS, 1001 ns) [NMRlipids simulation 643] alternateName: 1024DOPC_896CHOL_96000SOL_333K - description: Molecular dynamics trajectory of a lipid bilayer of 1024 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, 53 mol%) and 896 CHOL (cholesterol, 47 mol%) at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (495616 atoms). Deposited as NMRlipids Databank simulation 643 and available from https://doi.org/10.5281/zenodo.6943929. + description: Molecular dynamics trajectory of a lipid bilayer of 1024 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, + 53 mol%) and 896 CHOL (cholesterol, 47 mol%) at 333.15 K. Simulated with CHARMM36 + in GROMACS for 1001 ns (495616 atoms). Deposited as NMRlipids Databank simulation + 643 and available from https://doi.org/10.5281/zenodo.6943929. sameAs: https://doi.org/10.5281/zenodo.6943929 datePublished: '2022-07-30' license: diff --git a/Simulations/9ea/934/9ea93440f105cf86e2d9ce7c85339087d7080c7a/ad13ec526b21e9ce764d38d6279b1e535a61e55f/README.yaml b/Simulations/9ea/934/9ea93440f105cf86e2d9ce7c85339087d7080c7a/ad13ec526b21e9ce764d38d6279b1e535a61e55f/README.yaml index 831103a5d8..af04621afb 100644 --- a/Simulations/9ea/934/9ea93440f105cf86e2d9ce7c85339087d7080c7a/ad13ec526b21e9ce764d38d6279b1e535a61e55f/README.yaml +++ b/Simulations/9ea/934/9ea93440f105cf86e2d9ce7c85339087d7080c7a/ad13ec526b21e9ce764d38d6279b1e535a61e55f/README.yaml @@ -46,9 +46,12 @@ EXPERIMENT: - 10.1016/j.bbamem.2011.07.022/4 ID: 41 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC bilayer at 323 K (Berger-DPPC-98, GROMACS 4.6.6, 60 ns) [NMRlipids simulation 41] + name: Molecular dynamics trajectory of a DPPC bilayer at 323 K (Berger-DPPC-98, + GROMACS 4.6.6, 60 ns) [NMRlipids simulation 41] alternateName: 72DPPC_2880SOL_323K_Berger - description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) at 323 K. Simulated with Berger-DPPC-98 in GROMACS 4.6.6 for 60 ns (12240 atoms). Deposited as NMRlipids Databank simulation 41 and available from https://doi.org/10.5281/zenodo.13934. + description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) + at 323 K. Simulated with Berger-DPPC-98 in GROMACS 4.6.6 for 60 ns (12240 atoms). + Deposited as NMRlipids Databank simulation 41 and available from https://doi.org/10.5281/zenodo.13934. sameAs: https://doi.org/10.5281/zenodo.13934 datePublished: '2015-01-13' license: diff --git a/Simulations/9eb/3db/9eb3db5cf80e54ff238e5b91661ffb54013aee78/cfe9388d77646a60caa8c5147bc6087bb7e2ebb0/README.yaml b/Simulations/9eb/3db/9eb3db5cf80e54ff238e5b91661ffb54013aee78/cfe9388d77646a60caa8c5147bc6087bb7e2ebb0/README.yaml index b6695fc378..d84117a1b9 100644 --- a/Simulations/9eb/3db/9eb3db5cf80e54ff238e5b91661ffb54013aee78/cfe9388d77646a60caa8c5147bc6087bb7e2ebb0/README.yaml +++ b/Simulations/9eb/3db/9eb3db5cf80e54ff238e5b91661ffb54013aee78/cfe9388d77646a60caa8c5147bc6087bb7e2ebb0/README.yaml @@ -53,9 +53,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 285 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/DHMDMAB (81:10:10) bilayer at 313 K (Lipid14, GROMACS, 80 ns) [NMRlipids simulation 285] + name: Molecular dynamics trajectory of a POPC/CLA/DHMDMAB (81:10:10) bilayer at + 313 K (Lipid14, GROMACS, 80 ns) [NMRlipids simulation 285] alternateName: 100POPC_12DHMDMAB_6214SOL_12CLA_313K - description: Molecular dynamics trajectory of a lipid bilayer of 100 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 81 mol%), 12 CLA (10 mol%) and 12 DHMDMAB (dihexadecyldimethylammonium, 10 mol%) at 313 K. Simulated with Lipid14 in GROMACS for 80 ns (33338 atoms). Deposited as NMRlipids Databank simulation 285 and available from https://doi.org/10.5281/zenodo.1020240. + description: Molecular dynamics trajectory of a lipid bilayer of 100 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 81 mol%), 12 CLA (10 mol%) and 12 DHMDMAB (dihexadecyldimethylammonium, 10 mol%) + at 313 K. Simulated with Lipid14 in GROMACS for 80 ns (33338 atoms). Deposited + as NMRlipids Databank simulation 285 and available from https://doi.org/10.5281/zenodo.1020240. sameAs: https://doi.org/10.5281/zenodo.1020240 datePublished: '2017-10-18' license: @@ -144,7 +148,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1020240 identifier: 10.5281/zenodo.1020240 url: https://doi.org/10.5281/zenodo.1020240 - name: Popc Bilayer With 10% Of Dihexadecyldimethylammonium Simulated At T313K With The Lipid14 Model Using Gromacs + name: Popc Bilayer With 10% Of Dihexadecyldimethylammonium Simulated At T313K + With The Lipid14 Model Using Gromacs publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/9f0/749/9f0749a02b302d7633d0a07ddc92c783c5757bc9/3e9f6b62bdd9ab1829649c509ea8c69be65927eb/README.yaml b/Simulations/9f0/749/9f0749a02b302d7633d0a07ddc92c783c5757bc9/3e9f6b62bdd9ab1829649c509ea8c69be65927eb/README.yaml index 8fe8c688ab..489ee4931d 100644 --- a/Simulations/9f0/749/9f0749a02b302d7633d0a07ddc92c783c5757bc9/3e9f6b62bdd9ab1829649c509ea8c69be65927eb/README.yaml +++ b/Simulations/9f0/749/9f0749a02b302d7633d0a07ddc92c783c5757bc9/3e9f6b62bdd9ab1829649c509ea8c69be65927eb/README.yaml @@ -44,9 +44,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 802 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 300 K (OPLS4, GROMACS Desmond XXXX-X, 400 ns) [NMRlipids simulation 802] + name: Molecular dynamics trajectory of a POPC bilayer at 300 K (OPLS4, GROMACS Desmond + XXXX-X, 400 ns) [NMRlipids simulation 802] alternateName: 200POPC_1500SOL_300K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 300 K. Simulated with OPLS4 in GROMACS Desmond XXXX-X for 400 ns (31300 atoms). Deposited as NMRlipids Databank simulation 802 and available from https://doi.org/10.5281/zenodo.10948670. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 300 K. Simulated with OPLS4 in GROMACS Desmond XXXX-X for 400 ns (31300 atoms). + Deposited as NMRlipids Databank simulation 802 and available from https://doi.org/10.5281/zenodo.10948670. sameAs: https://doi.org/10.5281/zenodo.10948670 datePublished: '2024-04-09' license: diff --git a/Simulations/9f8/6db/9f86db3af0f6d4f1bf7a96bb0d47f13d2ba24fe4/e64562e0bc9611297bfabf7aef34df897d72e5c9/README.yaml b/Simulations/9f8/6db/9f86db3af0f6d4f1bf7a96bb0d47f13d2ba24fe4/e64562e0bc9611297bfabf7aef34df897d72e5c9/README.yaml index bcdd44ca6d..5e5e2296e3 100644 --- a/Simulations/9f8/6db/9f86db3af0f6d4f1bf7a96bb0d47f13d2ba24fe4/e64562e0bc9611297bfabf7aef34df897d72e5c9/README.yaml +++ b/Simulations/9f8/6db/9f86db3af0f6d4f1bf7a96bb0d47f13d2ba24fe4/e64562e0bc9611297bfabf7aef34df897d72e5c9/README.yaml @@ -52,9 +52,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/9 ID: 682 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (53:47) bilayer at 298.15 K (Slipids, GROMACS 2021, 1001 ns) [NMRlipids simulation 682] + name: Molecular dynamics trajectory of a POPC/CHOL (53:47) bilayer at 298.15 K (Slipids, + GROMACS 2021, 1001 ns) [NMRlipids simulation 682] alternateName: Slipids_POPC_CHOL47_L - description: Molecular dynamics trajectory of a lipid bilayer of 1024 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 53 mol%) and 896 CHOL (cholesterol, 47 mol%) at 298.15 K. Simulated with Slipids in GROMACS 2021 for 1001 ns (491520 atoms). Deposited as NMRlipids Databank simulation 682 and available from https://doi.org/10.5281/zenodo.7022749. + description: Molecular dynamics trajectory of a lipid bilayer of 1024 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 53 mol%) and 896 CHOL (cholesterol, 47 mol%) at 298.15 K. Simulated with Slipids + in GROMACS 2021 for 1001 ns (491520 atoms). Deposited as NMRlipids Databank simulation + 682 and available from https://doi.org/10.5281/zenodo.7022749. sameAs: https://doi.org/10.5281/zenodo.7022749 datePublished: '2022-08-23' license: diff --git a/Simulations/9fb/6b7/9fb6b706ea484f4171bb4f8b9689aa6a7251bec1/79dbc9ba2af6e1feb29e30e63455c4d2e08ade96/README.yaml b/Simulations/9fb/6b7/9fb6b706ea484f4171bb4f8b9689aa6a7251bec1/79dbc9ba2af6e1feb29e30e63455c4d2e08ade96/README.yaml index 7430d2dd97..51955f1256 100644 --- a/Simulations/9fb/6b7/9fb6b706ea484f4171bb4f8b9689aa6a7251bec1/79dbc9ba2af6e1feb29e30e63455c4d2e08ade96/README.yaml +++ b/Simulations/9fb/6b7/9fb6b706ea484f4171bb4f8b9689aa6a7251bec1/79dbc9ba2af6e1feb29e30e63455c4d2e08ade96/README.yaml @@ -50,9 +50,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 276 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (42:29:29) bilayer at 298 K (Orange, GROMACS 4.5, 120 ns) [NMRlipids simulation 276] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (42:29:29) bilayer at 298 + K (Orange, GROMACS 4.5, 120 ns) [NMRlipids simulation 276] alternateName: 72POPC_2780SOL_50CLA_50SOD_298K - description: Molecular dynamics trajectory of a lipid bilayer of 72 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 42 mol%), 50 CLA (29 mol%) and 50 SOD (29 mol%) at 298 K. Simulated with Orange in GROMACS 4.5 for 120 ns (12184 atoms). Deposited as NMRlipids Databank simulation 276 and available from https://doi.org/10.5281/zenodo.34497. + description: Molecular dynamics trajectory of a lipid bilayer of 72 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 42 mol%), 50 CLA (29 mol%) and 50 SOD (29 mol%) at 298 K. Simulated with Orange + in GROMACS 4.5 for 120 ns (12184 atoms). Deposited as NMRlipids Databank simulation + 276 and available from https://doi.org/10.5281/zenodo.34497. sameAs: https://doi.org/10.5281/zenodo.34497 datePublished: '2015-12-02' license: @@ -141,7 +145,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.34497 identifier: 10.5281/zenodo.34497 url: https://doi.org/10.5281/zenodo.34497 - name: Md Simulation Trajectory For Popc Bilayer With 1000Mm Nacl (Orange, Gromacs 4.5.) + name: Md Simulation Trajectory For Popc Bilayer With 1000Mm Nacl (Orange, Gromacs + 4.5.) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/9fb/e30/9fbe3004624648f5490c115eec164a4eede4fd19/51c5af18a423b221cdc5001aba679e7ee7c46268/README.yaml b/Simulations/9fb/e30/9fbe3004624648f5490c115eec164a4eede4fd19/51c5af18a423b221cdc5001aba679e7ee7c46268/README.yaml index a9a0664107..14e50ac3d3 100644 --- a/Simulations/9fb/e30/9fbe3004624648f5490c115eec164a4eede4fd19/51c5af18a423b221cdc5001aba679e7ee7c46268/README.yaml +++ b/Simulations/9fb/e30/9fbe3004624648f5490c115eec164a4eede4fd19/51c5af18a423b221cdc5001aba679e7ee7c46268/README.yaml @@ -48,9 +48,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 683 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (71:29) bilayer at 298.15 K (Lipid17, GROMACS 2021, 1001 ns) [NMRlipids simulation 683] + name: Molecular dynamics trajectory of a POPC/CHOL (71:29) bilayer at 298.15 K (Lipid17, + GROMACS 2021, 1001 ns) [NMRlipids simulation 683] alternateName: Lipid17_POPC_CHOL29_L - description: Molecular dynamics trajectory of a lipid bilayer of 1024 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 71 mol%) and 416 CHOL (cholesterol, 29 mol%) at 298.15 K. Simulated with Lipid17 in GROMACS 2021 for 1001 ns (384000 atoms). Deposited as NMRlipids Databank simulation 683 and available from https://doi.org/10.5281/zenodo.6992065. + description: Molecular dynamics trajectory of a lipid bilayer of 1024 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 71 mol%) and 416 CHOL (cholesterol, 29 mol%) at 298.15 K. Simulated with Lipid17 + in GROMACS 2021 for 1001 ns (384000 atoms). Deposited as NMRlipids Databank simulation + 683 and available from https://doi.org/10.5281/zenodo.6992065. sameAs: https://doi.org/10.5281/zenodo.6992065 datePublished: '2022-08-15' license: diff --git a/Simulations/a00/2c2/a002c28997069825fa42a6b751369d8062533e14/757216c36b032096aca0f434eba8799fcd5e3860/README.yaml b/Simulations/a00/2c2/a002c28997069825fa42a6b751369d8062533e14/757216c36b032096aca0f434eba8799fcd5e3860/README.yaml index 23f9da80d5..0add77f57b 100644 --- a/Simulations/a00/2c2/a002c28997069825fa42a6b751369d8062533e14/757216c36b032096aca0f434eba8799fcd5e3860/README.yaml +++ b/Simulations/a00/2c2/a002c28997069825fa42a6b751369d8062533e14/757216c36b032096aca0f434eba8799fcd5e3860/README.yaml @@ -40,9 +40,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 409 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC bilayer at 288 K (CHARMM36, GROMACS 2016.4, 50 ns) [NMRlipids simulation 409] + name: Molecular dynamics trajectory of a DPPC bilayer at 288 K (CHARMM36, GROMACS + 2016.4, 50 ns) [NMRlipids simulation 409] alternateName: 256DPPC_42642SOL_288K - description: Molecular dynamics trajectory of a lipid bilayer of 256 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) at 288 K. Simulated with CHARMM36 in GROMACS 2016.4 for 50 ns (161206 atoms). Deposited as NMRlipids Databank simulation 409 and available from https://doi.org/10.5281/zenodo.4522359. + description: Molecular dynamics trajectory of a lipid bilayer of 256 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) + at 288 K. Simulated with CHARMM36 in GROMACS 2016.4 for 50 ns (161206 atoms). + Deposited as NMRlipids Databank simulation 409 and available from https://doi.org/10.5281/zenodo.4522359. sameAs: https://doi.org/10.5281/zenodo.4522359 datePublished: '2021-02-09' license: diff --git a/Simulations/a0f/89c/a0f89cff51391cc296a4b48a1db3f23225a2cce8/6935e8bc80176a1db07288c9772acc3ebe6ec85c/README.yaml b/Simulations/a0f/89c/a0f89cff51391cc296a4b48a1db3f23225a2cce8/6935e8bc80176a1db07288c9772acc3ebe6ec85c/README.yaml index 7432360965..30fe1a3e22 100644 --- a/Simulations/a0f/89c/a0f89cff51391cc296a4b48a1db3f23225a2cce8/6935e8bc80176a1db07288c9772acc3ebe6ec85c/README.yaml +++ b/Simulations/a0f/89c/a0f89cff51391cc296a4b48a1db3f23225a2cce8/6935e8bc80176a1db07288c9772acc3ebe6ec85c/README.yaml @@ -50,9 +50,13 @@ EXPERIMENT: CHOL: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a DOPC/CHOL (53:47) bilayer at 333.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 644] + name: Molecular dynamics trajectory of a DOPC/CHOL (53:47) bilayer at 333.15 K (CHARMM36, + GROMACS, 1001 ns) [NMRlipids simulation 644] alternateName: 256DOPC_224CHOL_24000SOL_333K - description: Molecular dynamics trajectory of a lipid bilayer of 256 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, 53 mol%) and 224 CHOL (cholesterol, 47 mol%) at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (123904 atoms). Deposited as NMRlipids Databank simulation 644 and available from https://doi.org/10.5281/zenodo.6943929. + description: Molecular dynamics trajectory of a lipid bilayer of 256 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, + 53 mol%) and 224 CHOL (cholesterol, 47 mol%) at 333.15 K. Simulated with CHARMM36 + in GROMACS for 1001 ns (123904 atoms). Deposited as NMRlipids Databank simulation + 644 and available from https://doi.org/10.5281/zenodo.6943929. sameAs: https://doi.org/10.5281/zenodo.6943929 datePublished: '2022-07-30' license: diff --git a/Simulations/a11/ccd/a11ccdd137fcb388e9f50e560d4b11e12d9f2b08/cfb915e5c8e27261294a6df514841b90caff7584/README.yaml b/Simulations/a11/ccd/a11ccdd137fcb388e9f50e560d4b11e12d9f2b08/cfb915e5c8e27261294a6df514841b90caff7584/README.yaml index d03e7372d9..72785adae1 100644 --- a/Simulations/a11/ccd/a11ccdd137fcb388e9f50e560d4b11e12d9f2b08/cfb915e5c8e27261294a6df514841b90caff7584/README.yaml +++ b/Simulations/a11/ccd/a11ccdd137fcb388e9f50e560d4b11e12d9f2b08/cfb915e5c8e27261294a6df514841b90caff7584/README.yaml @@ -50,9 +50,13 @@ EXPERIMENT: CHOL: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a DOPC/CHOL (80:20) bilayer at 333.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 645] + name: Molecular dynamics trajectory of a DOPC/CHOL (80:20) bilayer at 333.15 K (CHARMM36, + GROMACS, 1001 ns) [NMRlipids simulation 645] alternateName: 256DOPC_64CHOL_16000SOL_333K - description: Molecular dynamics trajectory of a lipid bilayer of 256 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, 80 mol%) and 64 CHOL (cholesterol, 20 mol%) at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (88064 atoms). Deposited as NMRlipids Databank simulation 645 and available from https://doi.org/10.5281/zenodo.6943929. + description: Molecular dynamics trajectory of a lipid bilayer of 256 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, + 80 mol%) and 64 CHOL (cholesterol, 20 mol%) at 333.15 K. Simulated with CHARMM36 + in GROMACS for 1001 ns (88064 atoms). Deposited as NMRlipids Databank simulation + 645 and available from https://doi.org/10.5281/zenodo.6943929. sameAs: https://doi.org/10.5281/zenodo.6943929 datePublished: '2022-07-30' license: diff --git a/Simulations/a13/ae4/a13ae44c257c084ed57bf4dce443e7d6a4c941b3/e0538e4c3d56769b5fd2aff4c08555bb83111b2d/README.yaml b/Simulations/a13/ae4/a13ae44c257c084ed57bf4dce443e7d6a4c941b3/e0538e4c3d56769b5fd2aff4c08555bb83111b2d/README.yaml index 1050190944..e4da916308 100644 --- a/Simulations/a13/ae4/a13ae44c257c084ed57bf4dce443e7d6a4c941b3/e0538e4c3d56769b5fd2aff4c08555bb83111b2d/README.yaml +++ b/Simulations/a13/ae4/a13ae44c257c084ed57bf4dce443e7d6a4c941b3/e0538e4c3d56769b5fd2aff4c08555bb83111b2d/README.yaml @@ -44,9 +44,12 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/1 ID: 684 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 298.15 K (Lipid17, GROMACS 2021, 1001 ns) [NMRlipids simulation 684] + name: Molecular dynamics trajectory of a POPC bilayer at 298.15 K (Lipid17, GROMACS + 2021, 1001 ns) [NMRlipids simulation 684] alternateName: Lipid17_POPC_L - description: Molecular dynamics trajectory of a lipid bilayer of 1024 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 298.15 K. Simulated with Lipid17 in GROMACS 2021 for 1001 ns (290816 atoms). Deposited as NMRlipids Databank simulation 684 and available from https://doi.org/10.5281/zenodo.6992065. + description: Molecular dynamics trajectory of a lipid bilayer of 1024 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 298.15 K. Simulated with Lipid17 in GROMACS 2021 for 1001 ns (290816 atoms). + Deposited as NMRlipids Databank simulation 684 and available from https://doi.org/10.5281/zenodo.6992065. sameAs: https://doi.org/10.5281/zenodo.6992065 datePublished: '2022-08-15' license: diff --git a/Simulations/a1d/1ce/a1d1ce26a05e41216af050e363e0540da9528ac3/4aad649cb6def78cf0a3a5cffdc7ab2ef1d81e8f/README.yaml b/Simulations/a1d/1ce/a1d1ce26a05e41216af050e363e0540da9528ac3/4aad649cb6def78cf0a3a5cffdc7ab2ef1d81e8f/README.yaml index aa7ecf1822..3c095ff8ba 100644 --- a/Simulations/a1d/1ce/a1d1ce26a05e41216af050e363e0540da9528ac3/4aad649cb6def78cf0a3a5cffdc7ab2ef1d81e8f/README.yaml +++ b/Simulations/a1d/1ce/a1d1ce26a05e41216af050e363e0540da9528ac3/4aad649cb6def78cf0a3a5cffdc7ab2ef1d81e8f/README.yaml @@ -49,9 +49,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 274 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (83:9:9) bilayer at 350 K (Slipids for lipids and Smith & Dang for ions, GROMACS 4.6, 200 ns) [NMRlipids simulation 274] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (83:9:9) bilayer at 350 K + (Slipids for lipids and Smith & Dang for ions, GROMACS 4.6, 200 ns) [NMRlipids + simulation 274] alternateName: 200POPC_9000SOL_21SOD_21CLA_350K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 83 mol%), 21 CLA (9 mol%) and 21 SOD (9 mol%) at 350 K. Simulated with Slipids for lipids and Smith & Dang for ions in GROMACS 4.6 for 200 ns (53842 atoms). Deposited as NMRlipids Databank simulation 274 and available from https://doi.org/10.5281/zenodo.259335. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 83 mol%), 21 CLA (9 mol%) and 21 SOD (9 mol%) at 350 K. Simulated with Slipids + for lipids and Smith & Dang for ions in GROMACS 4.6 for 200 ns (53842 atoms). + Deposited as NMRlipids Databank simulation 274 and available from https://doi.org/10.5281/zenodo.259335. sameAs: https://doi.org/10.5281/zenodo.259335 datePublished: '2017-01-24' license: @@ -139,7 +144,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.259335 identifier: 10.5281/zenodo.259335 url: https://doi.org/10.5281/zenodo.259335 - name: Popc With Varying Amounts Of Cholesterol, 130 Mm Of Nacl. Slipids With Ions By Smith & Dang + name: Popc With Varying Amounts Of Cholesterol, 130 Mm Of Nacl. Slipids With Ions + By Smith & Dang publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/a24/99f/a2499f2021c1d99c37857b5e4edd9dd0a2d0fb48/dc3980599ca88c9e37d95a397ebe849c3ba859a1/README.yaml b/Simulations/a24/99f/a2499f2021c1d99c37857b5e4edd9dd0a2d0fb48/dc3980599ca88c9e37d95a397ebe849c3ba859a1/README.yaml index 9095a33368..3838534d3c 100644 --- a/Simulations/a24/99f/a2499f2021c1d99c37857b5e4edd9dd0a2d0fb48/dc3980599ca88c9e37d95a397ebe849c3ba859a1/README.yaml +++ b/Simulations/a24/99f/a2499f2021c1d99c37857b5e4edd9dd0a2d0fb48/dc3980599ca88c9e37d95a397ebe849c3ba859a1/README.yaml @@ -47,9 +47,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 865 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (45:36:18) bilayer at 300 K (OPLS3e, GROMACS Desmond of Schrödinger 2019-4, 1 ns) [NMRlipids simulation 865] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (45:36:18) bilayer at 300 + K (OPLS3e, GROMACS Desmond of Schrödinger 2019-4, 1 ns) [NMRlipids simulation + 865] alternateName: POPC, 44 w/l, 300 K, 0.5 M CaCl2 - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 45 mol%), 160 CLA (36 mol%) and 80 CAL (18 mol%) at 300 K. Simulated with OPLS3e in GROMACS Desmond of Schrödinger 2019-4 for 1 ns (53680 atoms). Deposited as NMRlipids Databank simulation 865 and available from https://doi.org/10.5281/zenodo.6618982. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 45 mol%), 160 CLA (36 mol%) and 80 CAL (18 mol%) at 300 K. Simulated with OPLS3e + in GROMACS Desmond of Schrödinger 2019-4 for 1 ns (53680 atoms). Deposited as + NMRlipids Databank simulation 865 and available from https://doi.org/10.5281/zenodo.6618982. sameAs: https://doi.org/10.5281/zenodo.6618982 datePublished: '2022-03-14' license: @@ -140,7 +145,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.6618982 identifier: 10.5281/zenodo.6618982 url: https://doi.org/10.5281/zenodo.6618982 - name: MD simulation of POPC bilayer with OPLS3e force field, 500 mM CaCl2 part 1 + name: MD simulation of POPC bilayer with OPLS3e force field, 500 mM CaCl2 part + 1 publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/a28/cca/a28ccaf41580ddc039fd5e42eb247df79c7cac64/5e51116eaff743dcd0be72838d8c7762973c93f9/README.yaml b/Simulations/a28/cca/a28ccaf41580ddc039fd5e42eb247df79c7cac64/5e51116eaff743dcd0be72838d8c7762973c93f9/README.yaml index 353994a487..be054b916b 100644 --- a/Simulations/a28/cca/a28ccaf41580ddc039fd5e42eb247df79c7cac64/5e51116eaff743dcd0be72838d8c7762973c93f9/README.yaml +++ b/Simulations/a28/cca/a28ccaf41580ddc039fd5e42eb247df79c7cac64/5e51116eaff743dcd0be72838d8c7762973c93f9/README.yaml @@ -47,9 +47,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 858 bioschema_properties: - name: Molecular dynamics trajectory of a CLA/POPC/CAL (47:29:24) bilayer at 300 K (OPLS3e, GROMACS Desmond of Schrödinger 2019-4, 1 ns) [NMRlipids simulation 858] + name: Molecular dynamics trajectory of a CLA/POPC/CAL (47:29:24) bilayer at 300 + K (OPLS3e, GROMACS Desmond of Schrödinger 2019-4, 1 ns) [NMRlipids simulation + 858] alternateName: POPC, 44 w/l, 300 K, 1 M CaCl2 - description: Molecular dynamics trajectory of a lipid bilayer of 320 CLA (47 mol%), 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 29 mol%) and 160 CAL (24 mol%) at 300 K. Simulated with OPLS3e in GROMACS Desmond of Schrödinger 2019-4 for 1 ns (53920 atoms). Deposited as NMRlipids Databank simulation 858 and available from https://doi.org/10.5281/zenodo.6619202. + description: Molecular dynamics trajectory of a lipid bilayer of 320 CLA (47 mol%), + 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 29 mol%) and 160 CAL + (24 mol%) at 300 K. Simulated with OPLS3e in GROMACS Desmond of Schrödinger 2019-4 + for 1 ns (53920 atoms). Deposited as NMRlipids Databank simulation 858 and available + from https://doi.org/10.5281/zenodo.6619202. sameAs: https://doi.org/10.5281/zenodo.6619202 datePublished: '2022-03-15' license: @@ -140,7 +146,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.6619202 identifier: 10.5281/zenodo.6619202 url: https://doi.org/10.5281/zenodo.6619202 - name: MD simulation of POPC bilayer with OPLS3e force field, 1000 mM CaCl2 part 2 + name: MD simulation of POPC bilayer with OPLS3e force field, 1000 mM CaCl2 part + 2 publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/a2f/610/a2f610b5a8dc1e35852958a438cacb6aa3260746/6417d50fcba54497315b53baaeef9114abbfd238/README.yaml b/Simulations/a2f/610/a2f610b5a8dc1e35852958a438cacb6aa3260746/6417d50fcba54497315b53baaeef9114abbfd238/README.yaml index 1b1e1b576c..2897e77bf6 100644 --- a/Simulations/a2f/610/a2f610b5a8dc1e35852958a438cacb6aa3260746/6417d50fcba54497315b53baaeef9114abbfd238/README.yaml +++ b/Simulations/a2f/610/a2f610b5a8dc1e35852958a438cacb6aa3260746/6417d50fcba54497315b53baaeef9114abbfd238/README.yaml @@ -63,9 +63,16 @@ EXPERIMENT: CHOL: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a CHOL/POPC/SM18/CLA/SOD (30:30:30:5:5) bilayer at 321.15 K (CHARMM36, GROMACS 2020.4 and 2021.4, 300 ns) [NMRlipids simulation 764] + name: Molecular dynamics trajectory of a CHOL/POPC/SM18/CLA/SOD (30:30:30:5:5) bilayer + at 321.15 K (CHARMM36, GROMACS 2020.4 and 2021.4, 300 ns) [NMRlipids simulation + 764] alternateName: POPC/SSM/CHOL bilayer in water (with ions), 321.15 K, NPT - description: Molecular dynamics trajectory of a lipid bilayer of 100 CHOL (cholesterol, 30 mol%), 100 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 30 mol%), 100 SM18 (N-stearoyl-D-erythro-sphingosylphosphorylcholine, 30 mol%), 18 CLA (5 mol%) and 18 SOD (5 mol%) at 321.15 K. Simulated with CHARMM36 in GROMACS 2020.4 and 2021.4 for 300 ns (61136 atoms). Deposited as NMRlipids Databank simulation 764 and available from https://doi.org/10.5281/zenodo.8337239. + description: Molecular dynamics trajectory of a lipid bilayer of 100 CHOL (cholesterol, + 30 mol%), 100 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 30 mol%), + 100 SM18 (N-stearoyl-D-erythro-sphingosylphosphorylcholine, 30 mol%), 18 CLA (5 + mol%) and 18 SOD (5 mol%) at 321.15 K. Simulated with CHARMM36 in GROMACS 2020.4 + and 2021.4 for 300 ns (61136 atoms). Deposited as NMRlipids Databank simulation + 764 and available from https://doi.org/10.5281/zenodo.8337239. sameAs: https://doi.org/10.5281/zenodo.8337239 datePublished: '2023-09-12' license: diff --git a/Simulations/a30/747/a307474e5995f2b78fe8c34a45f8255b59cef375/17c84076f3a8df16f1e29ab24b83e1e428275bf8/README.yaml b/Simulations/a30/747/a307474e5995f2b78fe8c34a45f8255b59cef375/17c84076f3a8df16f1e29ab24b83e1e428275bf8/README.yaml index 4731450979..f33ca93b28 100644 --- a/Simulations/a30/747/a307474e5995f2b78fe8c34a45f8255b59cef375/17c84076f3a8df16f1e29ab24b83e1e428275bf8/README.yaml +++ b/Simulations/a30/747/a307474e5995f2b78fe8c34a45f8255b59cef375/17c84076f3a8df16f1e29ab24b83e1e428275bf8/README.yaml @@ -41,9 +41,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 685 bioschema_properties: - name: Molecular dynamics trajectory of a DOPC bilayer at 298.15 K (CHARMM36, GROMACS 2021, 1001 ns) [NMRlipids simulation 685] + name: Molecular dynamics trajectory of a DOPC bilayer at 298.15 K (CHARMM36, GROMACS + 2021, 1001 ns) [NMRlipids simulation 685] alternateName: DOPC_L - description: Molecular dynamics trajectory of a lipid bilayer of 1024 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) at 298.15 K. Simulated with CHARMM36 in GROMACS 2021 for 1001 ns (294912 atoms). Deposited as NMRlipids Databank simulation 685 and available from https://doi.org/10.5281/zenodo.7103807. + description: Molecular dynamics trajectory of a lipid bilayer of 1024 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) + at 298.15 K. Simulated with CHARMM36 in GROMACS 2021 for 1001 ns (294912 atoms). + Deposited as NMRlipids Databank simulation 685 and available from https://doi.org/10.5281/zenodo.7103807. sameAs: https://doi.org/10.5281/zenodo.7103807 datePublished: '2022-09-22' license: diff --git a/Simulations/a33/b16/a33b16c62911e46c6cfeffc5c1cbf9eeb548da67/c8e02bee0bb725a95396e3d471060434dba329e6/README.yaml b/Simulations/a33/b16/a33b16c62911e46c6cfeffc5c1cbf9eeb548da67/c8e02bee0bb725a95396e3d471060434dba329e6/README.yaml index d29fed3970..311244faa9 100644 --- a/Simulations/a33/b16/a33b16c62911e46c6cfeffc5c1cbf9eeb548da67/c8e02bee0bb725a95396e3d471060434dba329e6/README.yaml +++ b/Simulations/a33/b16/a33b16c62911e46c6cfeffc5c1cbf9eeb548da67/c8e02bee0bb725a95396e3d471060434dba329e6/README.yaml @@ -52,9 +52,13 @@ EXPERIMENT: - 10.1039/C4SM00066H/3 ID: 443 bioschema_properties: - name: Molecular dynamics trajectory of a POPS/SOD (50:50) bilayer at 298 K (ECC-lipids, SPC water model, ECC-ions, GROMACS 2018.0, 1000 ns) [NMRlipids simulation 443] + name: Molecular dynamics trajectory of a POPS/SOD (50:50) bilayer at 298 K (ECC-lipids, + SPC water model, ECC-ions, GROMACS 2018.0, 1000 ns) [NMRlipids simulation 443] alternateName: 72POPS_3600SOL_72SOD_298K_ECC-lipid - description: Molecular dynamics trajectory of a lipid bilayer of 72 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 50 mol%) and 72 SOD (50 mol%) at 298 K. Simulated with ECC-lipids, SPC water model, ECC-ions in GROMACS 2018.0 for 1000 ns (20016 atoms). Deposited as NMRlipids Databank simulation 443 and available from https://doi.org/10.5281/zenodo.1488094. + description: Molecular dynamics trajectory of a lipid bilayer of 72 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, + 50 mol%) and 72 SOD (50 mol%) at 298 K. Simulated with ECC-lipids, SPC water model, + ECC-ions in GROMACS 2018.0 for 1000 ns (20016 atoms). Deposited as NMRlipids Databank + simulation 443 and available from https://doi.org/10.5281/zenodo.1488094. sameAs: https://doi.org/10.5281/zenodo.1488094 datePublished: '2018-11-14' license: @@ -149,7 +153,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1488094 identifier: 10.5281/zenodo.1488094 url: https://doi.org/10.5281/zenodo.1488094 - name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS (various mixtures) with ECC-lipids force field, and Na+ (K+) counterions + name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS + (various mixtures) with ECC-lipids force field, and Na+ (K+) counterions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/a36/8ed/a368ed3ac3d818a13d7b7e41ef6d228c39e65aaa/998d6107b6c03db9ee7bea52fc2a4fe47e36814f/README.yaml b/Simulations/a36/8ed/a368ed3ac3d818a13d7b7e41ef6d228c39e65aaa/998d6107b6c03db9ee7bea52fc2a4fe47e36814f/README.yaml index 13427941d7..b68a1557ab 100644 --- a/Simulations/a36/8ed/a368ed3ac3d818a13d7b7e41ef6d228c39e65aaa/998d6107b6c03db9ee7bea52fc2a4fe47e36814f/README.yaml +++ b/Simulations/a36/8ed/a368ed3ac3d818a13d7b7e41ef6d228c39e65aaa/998d6107b6c03db9ee7bea52fc2a4fe47e36814f/README.yaml @@ -44,9 +44,12 @@ EXPERIMENT: - 10.1016/j.bbamem.2011.07.022/11 ID: 93 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 313 K (ECC-lipids, GROMACS 5.1.4, 300 ns) [NMRlipids simulation 93] + name: Molecular dynamics trajectory of a POPC bilayer at 313 K (ECC-lipids, GROMACS + 5.1.4, 300 ns) [NMRlipids simulation 93] alternateName: 128POPC_6400SOL_313K_TIP4p-FBmodel - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 300 ns (42752 atoms). Deposited as NMRlipids Databank simulation 93 and available from https://doi.org/10.5281/zenodo.1118980. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 300 ns (42752 atoms). + Deposited as NMRlipids Databank simulation 93 and available from https://doi.org/10.5281/zenodo.1118980. sameAs: https://doi.org/10.5281/zenodo.1118980 datePublished: '2017-12-19' license: @@ -135,7 +138,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1118980 identifier: 10.5281/zenodo.1118980 url: https://doi.org/10.5281/zenodo.1118980 - name: Simulations Of Popc Lipid Bilayer In Water Solution At Various Nacl And Cacl2 Concentrations Using Ecc-Popc Force Field And Various Water Models + name: Simulations Of Popc Lipid Bilayer In Water Solution At Various Nacl And + Cacl2 Concentrations Using Ecc-Popc Force Field And Various Water Models publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/a3a/0de/a3a0ded0add42922c7cc7053c0ce04a1393babf8/29b917ed78df2dd6b117b3036c2c481e952185c9/README.yaml b/Simulations/a3a/0de/a3a0ded0add42922c7cc7053c0ce04a1393babf8/29b917ed78df2dd6b117b3036c2c481e952185c9/README.yaml index d85a6beb57..dddc1c0939 100644 --- a/Simulations/a3a/0de/a3a0ded0add42922c7cc7053c0ce04a1393babf8/29b917ed78df2dd6b117b3036c2c481e952185c9/README.yaml +++ b/Simulations/a3a/0de/a3a0ded0add42922c7cc7053c0ce04a1393babf8/29b917ed78df2dd6b117b3036c2c481e952185c9/README.yaml @@ -42,9 +42,12 @@ EXPERIMENT: - 10.1016/j.bbamem.2011.07.022/4 ID: 390 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC bilayer at 323 K (GAFFlipid, GROMACS 4.5, 50 ns) [NMRlipids simulation 390] + name: Molecular dynamics trajectory of a DPPC bilayer at 323 K (GAFFlipid, GROMACS + 4.5, 50 ns) [NMRlipids simulation 390] alternateName: 72DPPC_2197SOL_323K - description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) at 323 K. Simulated with GAFFlipid in GROMACS 4.5 for 50 ns (15951 atoms). Deposited as NMRlipids Databank simulation 390 and available from https://doi.org/10.5281/zenodo.15550. + description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) + at 323 K. Simulated with GAFFlipid in GROMACS 4.5 for 50 ns (15951 atoms). Deposited + as NMRlipids Databank simulation 390 and available from https://doi.org/10.5281/zenodo.15550. sameAs: https://doi.org/10.5281/zenodo.15550 datePublished: '2015-02-20' license: @@ -136,7 +139,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.15550 identifier: 10.5281/zenodo.15550 url: https://doi.org/10.5281/zenodo.15550 - name: Md Simulation Trajectory And Related Files For Dppc Bilayer (Gafflipid, Gromacs 4.5) + name: Md Simulation Trajectory And Related Files For Dppc Bilayer (Gafflipid, + Gromacs 4.5) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/a3d/f66/a3df66f326ff40b301fc96f980adb9bcc461bfb4/8c090fc702f8a04415326dc3f24c96db04c72274/README.yaml b/Simulations/a3d/f66/a3df66f326ff40b301fc96f980adb9bcc461bfb4/8c090fc702f8a04415326dc3f24c96db04c72274/README.yaml index e32c803119..ba96e75f9c 100644 --- a/Simulations/a3d/f66/a3df66f326ff40b301fc96f980adb9bcc461bfb4/8c090fc702f8a04415326dc3f24c96db04c72274/README.yaml +++ b/Simulations/a3d/f66/a3df66f326ff40b301fc96f980adb9bcc461bfb4/8c090fc702f8a04415326dc3f24c96db04c72274/README.yaml @@ -42,9 +42,12 @@ EXPERIMENT: DPPE: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a DPPE bilayer at 342 K (CHARMM36, GROMACS 2023.3, 100 ns) [NMRlipids simulation 846] + name: Molecular dynamics trajectory of a DPPE bilayer at 342 K (CHARMM36, GROMACS + 2023.3, 100 ns) [NMRlipids simulation 846] alternateName: DPPE in TIP3(Water) at 342K - description: Molecular dynamics trajectory of a lipid bilayer of 34 DPPE (1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine) at 342 K. Simulated with CHARMM36 in GROMACS 2023.3 for 100 ns (8119 atoms). Deposited as NMRlipids Databank simulation 846 and available from https://doi.org/10.5281/zenodo.15662847. + description: Molecular dynamics trajectory of a lipid bilayer of 34 DPPE (1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine) + at 342 K. Simulated with CHARMM36 in GROMACS 2023.3 for 100 ns (8119 atoms). Deposited + as NMRlipids Databank simulation 846 and available from https://doi.org/10.5281/zenodo.15662847. sameAs: https://doi.org/10.5281/zenodo.15662847 datePublished: '2025-11-01' license: diff --git a/Simulations/a48/859/a4885929c7f32ab1e404e4996c0a8c8194d7f9d6/96b44569491b7798a614371ba18bad1064dd7732/README.yaml b/Simulations/a48/859/a4885929c7f32ab1e404e4996c0a8c8194d7f9d6/96b44569491b7798a614371ba18bad1064dd7732/README.yaml index dc1de2bbb8..62f799633f 100644 --- a/Simulations/a48/859/a4885929c7f32ab1e404e4996c0a8c8194d7f9d6/96b44569491b7798a614371ba18bad1064dd7732/README.yaml +++ b/Simulations/a48/859/a4885929c7f32ab1e404e4996c0a8c8194d7f9d6/96b44569491b7798a614371ba18bad1064dd7732/README.yaml @@ -50,9 +50,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 594 bioschema_properties: - name: Molecular dynamics trajectory of a DLPC/CLA/SOD (81:9:9) bilayer at 310 K (CHARMM36, GROMACS 2019, 500 ns) [NMRlipids simulation 594] + name: Molecular dynamics trajectory of a DLPC/CLA/SOD (81:9:9) bilayer at 310 K + (CHARMM36, GROMACS 2019, 500 ns) [NMRlipids simulation 594] alternateName: 200DLPC_10000SOL_23SOD_23CLA - description: Molecular dynamics trajectory of a lipid bilayer of 200 DLPC (1,2-dilauroyl-sn-glycero-3-phosphocholine, 81 mol%), 23 CLA (9 mol%) and 23 SOD (9 mol%) at 310 K. Simulated with CHARMM36 in GROMACS 2019 for 500 ns (51246 atoms). Deposited as NMRlipids Databank simulation 594 and available from https://doi.org/10.5281/zenodo.3592499. + description: Molecular dynamics trajectory of a lipid bilayer of 200 DLPC (1,2-dilauroyl-sn-glycero-3-phosphocholine, + 81 mol%), 23 CLA (9 mol%) and 23 SOD (9 mol%) at 310 K. Simulated with CHARMM36 + in GROMACS 2019 for 500 ns (51246 atoms). Deposited as NMRlipids Databank simulation + 594 and available from https://doi.org/10.5281/zenodo.3592499. sameAs: https://doi.org/10.5281/zenodo.3592499 datePublished: '2019-12-24' license: diff --git a/Simulations/a4e/fdb/a4efdb7a7ccae460ff4105010697e8cf2ca30225/064e559bfabc2fb9eb2ce6397963f6319e255373/README.yaml b/Simulations/a4e/fdb/a4efdb7a7ccae460ff4105010697e8cf2ca30225/064e559bfabc2fb9eb2ce6397963f6319e255373/README.yaml index e5bb50003e..3e22a52376 100644 --- a/Simulations/a4e/fdb/a4efdb7a7ccae460ff4105010697e8cf2ca30225/064e559bfabc2fb9eb2ce6397963f6319e255373/README.yaml +++ b/Simulations/a4e/fdb/a4efdb7a7ccae460ff4105010697e8cf2ca30225/064e559bfabc2fb9eb2ce6397963f6319e255373/README.yaml @@ -62,9 +62,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 370 bioschema_properties: - name: Molecular dynamics trajectory of a POT/POPC/CLA/POPS (34:32:25:8) bilayer at 310 K (Berger, GROMACS 4.0.7, 50 ns) [NMRlipids simulation 370] + name: Molecular dynamics trajectory of a POT/POPC/CLA/POPS (34:32:25:8) bilayer + at 310 K (Berger, GROMACS 4.0.7, 50 ns) [NMRlipids simulation 370] alternateName: 102POPC_22POPS_4290SOL_106POT_80CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 106 POT (34 mol%), 102 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 32 mol%), 80 CLA (25 mol%) and 26 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 8 mol%) at 310 K. Simulated with Berger in GROMACS 4.0.7 for 50 ns (19790 atoms). Deposited as NMRlipids Databank simulation 370 and available from https://doi.org/10.5281/zenodo.838225. + description: Molecular dynamics trajectory of a lipid bilayer of 106 POT (34 mol%), + 102 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 32 mol%), 80 CLA (25 + mol%) and 26 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 8 mol%) + at 310 K. Simulated with Berger in GROMACS 4.0.7 for 50 ns (19790 atoms). Deposited + as NMRlipids Databank simulation 370 and available from https://doi.org/10.5281/zenodo.838225. sameAs: https://doi.org/10.5281/zenodo.838225 datePublished: '2017-08-02' license: @@ -157,7 +162,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.838225 identifier: 10.5281/zenodo.838225 url: https://doi.org/10.5281/zenodo.838225 - name: Md Simulation Trajectory Of A Popc/Pops (4:1) Bilayer With 1M Kcl, Berger Force Field For Lipids, Dang'S For K+ And Ffgmx For Cl- + name: Md Simulation Trajectory Of A Popc/Pops (4:1) Bilayer With 1M Kcl, Berger + Force Field For Lipids, Dang'S For K+ And Ffgmx For Cl- publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/a50/c1a/a50c1a131bc220af7d5cc8d1ebb212f98b866101/f54cd09a11c7d3c5a2e470823a4d1b83c54c1c55/README.yaml b/Simulations/a50/c1a/a50c1a131bc220af7d5cc8d1ebb212f98b866101/f54cd09a11c7d3c5a2e470823a4d1b83c54c1c55/README.yaml index 962529db95..d85bbb0bd2 100644 --- a/Simulations/a50/c1a/a50c1a131bc220af7d5cc8d1ebb212f98b866101/f54cd09a11c7d3c5a2e470823a4d1b83c54c1c55/README.yaml +++ b/Simulations/a50/c1a/a50c1a131bc220af7d5cc8d1ebb212f98b866101/f54cd09a11c7d3c5a2e470823a4d1b83c54c1c55/README.yaml @@ -55,9 +55,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 324 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/SOD/CLA/POPS (35:32:25:7) bilayer at 298 K (CHARMM36, GROMACS, 150 ns) [NMRlipids simulation 324] + name: Molecular dynamics trajectory of a POPC/SOD/CLA/POPS (35:32:25:7) bilayer + at 298 K (CHARMM36, GROMACS, 150 ns) [NMRlipids simulation 324] alternateName: 110POPC_22POPS_4932SOL_101SOD_79CLA_298K - description: Molecular dynamics trajectory of a lipid bilayer of 110 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 35 mol%), 101 SOD (32 mol%), 79 CLA (25 mol%) and 22 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 7 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for 150 ns (32510 atoms). Deposited as NMRlipids Databank simulation 324 and available from https://doi.org/10.5281/zenodo.1493229. + description: Molecular dynamics trajectory of a lipid bilayer of 110 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 35 mol%), 101 SOD (32 mol%), 79 CLA (25 mol%) and 22 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, + 7 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for 150 ns (32510 atoms). + Deposited as NMRlipids Databank simulation 324 and available from https://doi.org/10.5281/zenodo.1493229. sameAs: https://doi.org/10.5281/zenodo.1493229 datePublished: '2018-11-21' license: diff --git a/Simulations/a52/e79/a52e79dbc82812b1b5c164c0f2b9fdc9c76da24a/b6e1524a8df1bab25ae7b4e69a242d6e1bc0fcda/README.yaml b/Simulations/a52/e79/a52e79dbc82812b1b5c164c0f2b9fdc9c76da24a/b6e1524a8df1bab25ae7b4e69a242d6e1bc0fcda/README.yaml index faed808d91..5120432f6f 100644 --- a/Simulations/a52/e79/a52e79dbc82812b1b5c164c0f2b9fdc9c76da24a/b6e1524a8df1bab25ae7b4e69a242d6e1bc0fcda/README.yaml +++ b/Simulations/a52/e79/a52e79dbc82812b1b5c164c0f2b9fdc9c76da24a/b6e1524a8df1bab25ae7b4e69a242d6e1bc0fcda/README.yaml @@ -47,9 +47,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 861 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (89:7:4) bilayer at 300 K (OPLS3e, GROMACS Desmond of Schrödinger 2019-4, 500 ns) [NMRlipids simulation 861] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (89:7:4) bilayer at 300 K + (OPLS3e, GROMACS Desmond of Schrödinger 2019-4, 500 ns) [NMRlipids simulation + 861] alternateName: POPC, 44 w/l, 300 K, 0.05 M CaCl2 - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 89 mol%), 16 CLA (7 mol%) and 8 CAL (4 mol%) at 300 K. Simulated with OPLS3e in GROMACS Desmond of Schrödinger 2019-4 for 500 ns (53464 atoms). Deposited as NMRlipids Databank simulation 861 and available from https://doi.org/10.5281/zenodo.10212566. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 89 mol%), 16 CLA (7 mol%) and 8 CAL (4 mol%) at 300 K. Simulated with OPLS3e in + GROMACS Desmond of Schrödinger 2019-4 for 500 ns (53464 atoms). Deposited as NMRlipids + Databank simulation 861 and available from https://doi.org/10.5281/zenodo.10212566. sameAs: https://doi.org/10.5281/zenodo.10212566 datePublished: '2022' license: @@ -140,7 +145,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.10212566 identifier: 10.5281/zenodo.10212566 url: https://doi.org/10.5281/zenodo.10212566 - name: MD simulation of POPC bilayer with OPLS3e force field, 50 mM CaCl2 part 1 + name: MD simulation of POPC bilayer with OPLS3e force field, 50 mM CaCl2 part + 1 publisher: Zenodo _source: api: datacite diff --git a/Simulations/a54/7b0/a547b02ef91a5326e662914a355ca63b56ecfd1e/5ec971904820709ec27906670170e3ee827f72ea/README.yaml b/Simulations/a54/7b0/a547b02ef91a5326e662914a355ca63b56ecfd1e/5ec971904820709ec27906670170e3ee827f72ea/README.yaml index 54e575b29e..a7152c4b98 100644 --- a/Simulations/a54/7b0/a547b02ef91a5326e662914a355ca63b56ecfd1e/5ec971904820709ec27906670170e3ee827f72ea/README.yaml +++ b/Simulations/a54/7b0/a547b02ef91a5326e662914a355ca63b56ecfd1e/5ec971904820709ec27906670170e3ee827f72ea/README.yaml @@ -55,9 +55,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 333 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/CHOL/CLA/SOD (65:17:9:9) bilayer at 310 K (Slipids, GROMACS, 300 ns) [NMRlipids simulation 333] + name: Molecular dynamics trajectory of a DPPC/CHOL/CLA/SOD (65:17:9:9) bilayer at + 310 K (Slipids, GROMACS, 300 ns) [NMRlipids simulation 333] alternateName: 912DPPC_240CHOL_46440SOL_124SOD_124CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 912 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 65 mol%), 240 CHOL (cholesterol, 17 mol%), 124 CLA (9 mol%) and 124 SOD (9 mol%) at 310 K. Simulated with Slipids in GROMACS for 300 ns (275888 atoms). Deposited as NMRlipids Databank simulation 333 and available from https://doi.org/10.5281/zenodo.3540513. + description: Molecular dynamics trajectory of a lipid bilayer of 912 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 65 mol%), 240 CHOL (cholesterol, 17 mol%), 124 CLA (9 mol%) and 124 SOD (9 mol%) + at 310 K. Simulated with Slipids in GROMACS for 300 ns (275888 atoms). Deposited + as NMRlipids Databank simulation 333 and available from https://doi.org/10.5281/zenodo.3540513. sameAs: https://doi.org/10.5281/zenodo.3540513 datePublished: '2019-11-13' license: diff --git a/Simulations/a54/7b0/a547b02ef91a5326e662914a355ca63b56ecfd1e/b9d0922a6884cade34ebf60415bbc7e143db1947/README.yaml b/Simulations/a54/7b0/a547b02ef91a5326e662914a355ca63b56ecfd1e/b9d0922a6884cade34ebf60415bbc7e143db1947/README.yaml index 9c21e792c9..a1541dcf04 100644 --- a/Simulations/a54/7b0/a547b02ef91a5326e662914a355ca63b56ecfd1e/b9d0922a6884cade34ebf60415bbc7e143db1947/README.yaml +++ b/Simulations/a54/7b0/a547b02ef91a5326e662914a355ca63b56ecfd1e/b9d0922a6884cade34ebf60415bbc7e143db1947/README.yaml @@ -56,9 +56,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 332 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/CHOL/CLA/SOD (65:17:9:9) bilayer at 310 K (Slipids, GROMACS 4.6, 500 ns) [NMRlipids simulation 332] + name: Molecular dynamics trajectory of a DPPC/CHOL/CLA/SOD (65:17:9:9) bilayer at + 310 K (Slipids, GROMACS 4.6, 500 ns) [NMRlipids simulation 332] alternateName: 912DPPC_240CHOL_46440SOL_124SOD_124CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 912 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 65 mol%), 240 CHOL (cholesterol, 17 mol%), 124 CLA (9 mol%) and 124 SOD (9 mol%) at 310 K. Simulated with Slipids in GROMACS 4.6 for 500 ns (275888 atoms). Deposited as NMRlipids Databank simulation 332 and available from https://doi.org/10.5281/zenodo.439080. + description: Molecular dynamics trajectory of a lipid bilayer of 912 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 65 mol%), 240 CHOL (cholesterol, 17 mol%), 124 CLA (9 mol%) and 124 SOD (9 mol%) + at 310 K. Simulated with Slipids in GROMACS 4.6 for 500 ns (275888 atoms). Deposited + as NMRlipids Databank simulation 332 and available from https://doi.org/10.5281/zenodo.439080. sameAs: https://doi.org/10.5281/zenodo.439080 datePublished: '2017-03-29' license: @@ -152,7 +156,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.439080 identifier: 10.5281/zenodo.439080 url: https://doi.org/10.5281/zenodo.439080 - name: Simulations Of Dppc/Cholesterol Bilayers With The Slipids Force Field, Part 2/2 + name: Simulations Of Dppc/Cholesterol Bilayers With The Slipids Force Field, Part + 2/2 publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/a57/e4d/a57e4da040747acbd9359130fca371ad3ca22854/54be9ccd66f7f57a53eb9e8266ca530a320db3e2/README.yaml b/Simulations/a57/e4d/a57e4da040747acbd9359130fca371ad3ca22854/54be9ccd66f7f57a53eb9e8266ca530a320db3e2/README.yaml index bfb3806b0c..e11b25c72b 100644 --- a/Simulations/a57/e4d/a57e4da040747acbd9359130fca371ad3ca22854/54be9ccd66f7f57a53eb9e8266ca530a320db3e2/README.yaml +++ b/Simulations/a57/e4d/a57e4da040747acbd9359130fca371ad3ca22854/54be9ccd66f7f57a53eb9e8266ca530a320db3e2/README.yaml @@ -50,9 +50,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 560 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (58:21:21) bilayer at 298 K (Orange, GROMACS 4.5, 120 ns) [NMRlipids simulation 560] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (58:21:21) bilayer at 298 + K (Orange, GROMACS 4.5, 120 ns) [NMRlipids simulation 560] alternateName: 72POPC_2802SOL_26CLA_26SOD_298K - description: Molecular dynamics trajectory of a lipid bilayer of 72 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 58 mol%), 26 CLA (21 mol%) and 26 SOD (21 mol%) at 298 K. Simulated with Orange in GROMACS 4.5 for 120 ns (12202 atoms). Deposited as NMRlipids Databank simulation 560 and available from https://doi.org/10.5281/zenodo.34490. + description: Molecular dynamics trajectory of a lipid bilayer of 72 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 58 mol%), 26 CLA (21 mol%) and 26 SOD (21 mol%) at 298 K. Simulated with Orange + in GROMACS 4.5 for 120 ns (12202 atoms). Deposited as NMRlipids Databank simulation + 560 and available from https://doi.org/10.5281/zenodo.34490. sameAs: https://doi.org/10.5281/zenodo.34490 datePublished: '2015-12-02' license: @@ -141,7 +145,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.34490 identifier: 10.5281/zenodo.34490 url: https://doi.org/10.5281/zenodo.34490 - name: Md Simulation Trajectory For Popc Bilayer With 510Mm Nacl (Orange, Gromacs 4.5.) + name: Md Simulation Trajectory For Popc Bilayer With 510Mm Nacl (Orange, Gromacs + 4.5.) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/a5b/236/a5b236bf329671e10e32c2fc798fb7a3a5136db6/57b957fbea76919f972a818e2f0de55363f89717/README.yaml b/Simulations/a5b/236/a5b236bf329671e10e32c2fc798fb7a3a5136db6/57b957fbea76919f972a818e2f0de55363f89717/README.yaml index a37277111d..da57b6b50e 100644 --- a/Simulations/a5b/236/a5b236bf329671e10e32c2fc798fb7a3a5136db6/57b957fbea76919f972a818e2f0de55363f89717/README.yaml +++ b/Simulations/a5b/236/a5b236bf329671e10e32c2fc798fb7a3a5136db6/57b957fbea76919f972a818e2f0de55363f89717/README.yaml @@ -49,9 +49,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 268 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (83:9:9) bilayer at 330 K (Slipids for lipids and Smith & Dang for ions, GROMACS 4.6, 200 ns) [NMRlipids simulation 268] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (83:9:9) bilayer at 330 K + (Slipids for lipids and Smith & Dang for ions, GROMACS 4.6, 200 ns) [NMRlipids + simulation 268] alternateName: 200POPC_9000SOL_21SOD_21CLA_330K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 83 mol%), 21 CLA (9 mol%) and 21 SOD (9 mol%) at 330 K. Simulated with Slipids for lipids and Smith & Dang for ions in GROMACS 4.6 for 200 ns (53842 atoms). Deposited as NMRlipids Databank simulation 268 and available from https://doi.org/10.5281/zenodo.259335. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 83 mol%), 21 CLA (9 mol%) and 21 SOD (9 mol%) at 330 K. Simulated with Slipids + for lipids and Smith & Dang for ions in GROMACS 4.6 for 200 ns (53842 atoms). + Deposited as NMRlipids Databank simulation 268 and available from https://doi.org/10.5281/zenodo.259335. sameAs: https://doi.org/10.5281/zenodo.259335 datePublished: '2017-01-24' license: @@ -139,7 +144,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.259335 identifier: 10.5281/zenodo.259335 url: https://doi.org/10.5281/zenodo.259335 - name: Popc With Varying Amounts Of Cholesterol, 130 Mm Of Nacl. Slipids With Ions By Smith & Dang + name: Popc With Varying Amounts Of Cholesterol, 130 Mm Of Nacl. Slipids With Ions + By Smith & Dang publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/a63/ca7/a63ca7001cbd5cfc328da122668d1aebc00f2c91/220540156a6ac7813942fd01d998a491b6ff9b8b/README.yaml b/Simulations/a63/ca7/a63ca7001cbd5cfc328da122668d1aebc00f2c91/220540156a6ac7813942fd01d998a491b6ff9b8b/README.yaml index 40964546ad..a3e9f3e466 100644 --- a/Simulations/a63/ca7/a63ca7001cbd5cfc328da122668d1aebc00f2c91/220540156a6ac7813942fd01d998a491b6ff9b8b/README.yaml +++ b/Simulations/a63/ca7/a63ca7001cbd5cfc328da122668d1aebc00f2c91/220540156a6ac7813942fd01d998a491b6ff9b8b/README.yaml @@ -46,9 +46,12 @@ DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 558 AUTHORS_CONTACT: Papadopoulos, Chris; Fuchs, Patrick F.J. bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 300 K (CHARMM36, GROMACS, 300 ns) [NMRlipids simulation 558] + name: Molecular dynamics trajectory of a POPC bilayer at 300 K (CHARMM36, GROMACS, + 300 ns) [NMRlipids simulation 558] alternateName: POPC_T300K - description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 300 K. Simulated with CHARMM36 in GROMACS for 300 ns (63605 atoms). Deposited as NMRlipids Databank simulation 558 and available from https://doi.org/10.5281/zenodo.1306800. + description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 300 K. Simulated with CHARMM36 in GROMACS for 300 ns (63605 atoms). Deposited + as NMRlipids Databank simulation 558 and available from https://doi.org/10.5281/zenodo.1306800. sameAs: https://doi.org/10.5281/zenodo.1306800 datePublished: '2018-07-06' license: diff --git a/Simulations/a67/ed5/a67ed535bd6273fbcb24c2f920c6802bbefeead9/d7dff31de894f985d1400447eeeeca7ecce66688/README.yaml b/Simulations/a67/ed5/a67ed535bd6273fbcb24c2f920c6802bbefeead9/d7dff31de894f985d1400447eeeeca7ecce66688/README.yaml index a50dc91816..7d8ddbbd65 100644 --- a/Simulations/a67/ed5/a67ed535bd6273fbcb24c2f920c6802bbefeead9/d7dff31de894f985d1400447eeeeca7ecce66688/README.yaml +++ b/Simulations/a67/ed5/a67ed535bd6273fbcb24c2f920c6802bbefeead9/d7dff31de894f985d1400447eeeeca7ecce66688/README.yaml @@ -51,9 +51,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 420 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (80:10:10) bilayer at 310.15 K (CHARMM36, GROMACS, 432 ns) [NMRlipids simulation 420] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (80:10:10) bilayer at 310.15 + K (CHARMM36, GROMACS, 432 ns) [NMRlipids simulation 420] alternateName: 200POPC_9000SOL_25SOD_25CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 80 mol%), 25 CLA (10 mol%) and 25 SOD (10 mol%) at 310.15 K. Simulated with CHARMM36 in GROMACS for 432 ns (53850 atoms). Deposited as NMRlipids Databank simulation 420 and available from https://doi.org/10.5281/zenodo.3434396. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 80 mol%), 25 CLA (10 mol%) and 25 SOD (10 mol%) at 310.15 K. Simulated with CHARMM36 + in GROMACS for 432 ns (53850 atoms). Deposited as NMRlipids Databank simulation + 420 and available from https://doi.org/10.5281/zenodo.3434396. sameAs: https://doi.org/10.5281/zenodo.3434396 datePublished: '2019-09-17' license: diff --git a/Simulations/a69/b1f/a69b1f89e3c9dd265a7ac3009eceb75695de582b/51b9a8cb6e4f8c4f17816bfcc025978b93276e5d/README.yaml b/Simulations/a69/b1f/a69b1f89e3c9dd265a7ac3009eceb75695de582b/51b9a8cb6e4f8c4f17816bfcc025978b93276e5d/README.yaml index 9ca7fe191a..f5d890b042 100644 --- a/Simulations/a69/b1f/a69b1f89e3c9dd265a7ac3009eceb75695de582b/51b9a8cb6e4f8c4f17816bfcc025978b93276e5d/README.yaml +++ b/Simulations/a69/b1f/a69b1f89e3c9dd265a7ac3009eceb75695de582b/51b9a8cb6e4f8c4f17816bfcc025978b93276e5d/README.yaml @@ -63,9 +63,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 112 bioschema_properties: - name: Molecular dynamics trajectory of a CLA/DMTAP/DMPC/SOD (43:39:13:4) bilayer at 323 K (Berger with DMTAP modification by Gurtovenko et al., GROMACS 3.x, 110 ns) [NMRlipids simulation 112] + name: Molecular dynamics trajectory of a CLA/DMTAP/DMPC/SOD (43:39:13:4) bilayer + at 323 K (Berger with DMTAP modification by Gurtovenko et al., GROMACS 3.x, 110 + ns) [NMRlipids simulation 112] alternateName: 32DMPC_96DMTAP_10SOD_106CLA_5476SOL_323K - description: Molecular dynamics trajectory of a lipid bilayer of 106 CLA (43 mol%), 96 DMTAP (1,2-dimyristoyl-3-trimethylammonium-propane, 39 mol%), 32 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine, 13 mol%) and 10 SOD (4 mol%) at 323 K. Simulated with Berger with DMTAP modification by Gurtovenko et al. in GROMACS 3.x for 110 ns (21760 atoms). Deposited as NMRlipids Databank simulation 112 and available from https://doi.org/10.5281/zenodo.51760. + description: Molecular dynamics trajectory of a lipid bilayer of 106 CLA (43 mol%), + 96 DMTAP (1,2-dimyristoyl-3-trimethylammonium-propane, 39 mol%), 32 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine, + 13 mol%) and 10 SOD (4 mol%) at 323 K. Simulated with Berger with DMTAP modification + by Gurtovenko et al. in GROMACS 3.x for 110 ns (21760 atoms). Deposited as NMRlipids + Databank simulation 112 and available from https://doi.org/10.5281/zenodo.51760. sameAs: https://doi.org/10.5281/zenodo.51760 datePublished: '2016-05-20' license: @@ -164,7 +170,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.51760 identifier: 10.5281/zenodo.51760 url: https://doi.org/10.5281/zenodo.51760 - name: 'Molecular dynamics simulation trajectory of a cationic lipid bilayer: 75/25 mol% DMTAP/DMPC in 0.1 M NaCl' + name: 'Molecular dynamics simulation trajectory of a cationic lipid bilayer: 75/25 + mol% DMTAP/DMPC in 0.1 M NaCl' publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/a71/1f1/a711f1339b988a9e4268e6f598879fa581a51302/88f921d19a94ca3af98fe79d5079af15161350fc/README.yaml b/Simulations/a71/1f1/a711f1339b988a9e4268e6f598879fa581a51302/88f921d19a94ca3af98fe79d5079af15161350fc/README.yaml index 0e8af4b1d5..07cfc7d866 100644 --- a/Simulations/a71/1f1/a711f1339b988a9e4268e6f598879fa581a51302/88f921d19a94ca3af98fe79d5079af15161350fc/README.yaml +++ b/Simulations/a71/1f1/a711f1339b988a9e4268e6f598879fa581a51302/88f921d19a94ca3af98fe79d5079af15161350fc/README.yaml @@ -43,9 +43,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 547 bioschema_properties: - name: Molecular dynamics trajectory of a DOPC bilayer at 323.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 547] + name: Molecular dynamics trajectory of a DOPC bilayer at 323.15 K (CHARMM36, GROMACS, + 1001 ns) [NMRlipids simulation 547] alternateName: 64DOPC_3200SOL_323K - description: Molecular dynamics trajectory of a lipid bilayer of 64 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) at 323.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (18432 atoms). Deposited as NMRlipids Databank simulation 547 and available from https://doi.org/10.5281/zenodo.6943086. + description: Molecular dynamics trajectory of a lipid bilayer of 64 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) + at 323.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (18432 atoms). Deposited + as NMRlipids Databank simulation 547 and available from https://doi.org/10.5281/zenodo.6943086. sameAs: https://doi.org/10.5281/zenodo.6943086 datePublished: '2022-07-30' license: diff --git a/Simulations/a71/d54/a71d54feeb142784debeffbade25b7b6e037a80a/4787a89478d4806c2111a211f4af8bb0715e927d/README.yaml b/Simulations/a71/d54/a71d54feeb142784debeffbade25b7b6e037a80a/4787a89478d4806c2111a211f4af8bb0715e927d/README.yaml index 78063d5803..eb921655a7 100644 --- a/Simulations/a71/d54/a71d54feeb142784debeffbade25b7b6e037a80a/4787a89478d4806c2111a211f4af8bb0715e927d/README.yaml +++ b/Simulations/a71/d54/a71d54feeb142784debeffbade25b7b6e037a80a/4787a89478d4806c2111a211f4af8bb0715e927d/README.yaml @@ -43,9 +43,13 @@ SOFTWARE: gromacs DIR_WRK: /usr/home/bort/Databank ID: 548 bioschema_properties: - name: Molecular dynamics trajectory of a DOPS/SOD (50:50) bilayer at 303 K (Slipids, GROMACS, 100 ns) [NMRlipids simulation 548] + name: Molecular dynamics trajectory of a DOPS/SOD (50:50) bilayer at 303 K (Slipids, + GROMACS, 100 ns) [NMRlipids simulation 548] alternateName: 128DOPS_4880SOL_128SOD_303K_v1 - description: Molecular dynamics trajectory of a lipid bilayer of 128 DOPS (1,2-dioleoyl-sn-glycero-3-phospho-L-serine, 50 mol%) and 128 SOD (50 mol%) at 303 K. Simulated with Slipids in GROMACS for 100 ns (30336 atoms). Deposited as NMRlipids Databank simulation 548 and available from https://doi.org/10.5281/zenodo.1129439. + description: Molecular dynamics trajectory of a lipid bilayer of 128 DOPS (1,2-dioleoyl-sn-glycero-3-phospho-L-serine, + 50 mol%) and 128 SOD (50 mol%) at 303 K. Simulated with Slipids in GROMACS for + 100 ns (30336 atoms). Deposited as NMRlipids Databank simulation 548 and available + from https://doi.org/10.5281/zenodo.1129439. sameAs: https://doi.org/10.5281/zenodo.1129439 datePublished: '2017-12-24' license: diff --git a/Simulations/a7e/178/a7e1783cd2c8124d8f0acf0b35700ec2596ff889/fbb2bece23092fce438a7a236b421af208f287eb/README.yaml b/Simulations/a7e/178/a7e1783cd2c8124d8f0acf0b35700ec2596ff889/fbb2bece23092fce438a7a236b421af208f287eb/README.yaml index 6775925a1d..80c356c16a 100644 --- a/Simulations/a7e/178/a7e1783cd2c8124d8f0acf0b35700ec2596ff889/fbb2bece23092fce438a7a236b421af208f287eb/README.yaml +++ b/Simulations/a7e/178/a7e1783cd2c8124d8f0acf0b35700ec2596ff889/fbb2bece23092fce438a7a236b421af208f287eb/README.yaml @@ -54,9 +54,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 870 bioschema_properties: - name: Molecular dynamics trajectory of a NH4/POPI/POPC (44:44:11) bilayer at 310 K (CHARMM36, GROMACS 2022.4, 500 ns) [NMRlipids simulation 870] + name: Molecular dynamics trajectory of a NH4/POPI/POPC (44:44:11) bilayer at 310 + K (CHARMM36, GROMACS 2022.4, 500 ns) [NMRlipids simulation 870] alternateName: POPI-POPC (80:20), full hydration, 310 K, NH4+ counter ions - description: Molecular dynamics trajectory of a lipid bilayer of 160 NH4 (44 mol%), 160 POPI (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoinositol, 44 mol%) and 40 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 11 mol%) at 310 K. Simulated with CHARMM36 in GROMACS 2022.4 for 500 ns (58080 atoms). Deposited as NMRlipids Databank simulation 870 and available from https://doi.org/10.5281/zenodo.10253820. + description: Molecular dynamics trajectory of a lipid bilayer of 160 NH4 (44 mol%), + 160 POPI (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoinositol, 44 mol%) and 40 POPC + (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 11 mol%) at 310 K. Simulated + with CHARMM36 in GROMACS 2022.4 for 500 ns (58080 atoms). Deposited as NMRlipids + Databank simulation 870 and available from https://doi.org/10.5281/zenodo.10253820. sameAs: https://doi.org/10.5281/zenodo.10253820 datePublished: '2023-12-18' license: diff --git a/Simulations/a7e/c6d/a7ec6ded506e2f92f704630d74da8d5d0bf9441c/23177d5f6629268724e6e25a19047c3d3f65dc8d/README.yaml b/Simulations/a7e/c6d/a7ec6ded506e2f92f704630d74da8d5d0bf9441c/23177d5f6629268724e6e25a19047c3d3f65dc8d/README.yaml index 9141baba6c..5303a481ca 100644 --- a/Simulations/a7e/c6d/a7ec6ded506e2f92f704630d74da8d5d0bf9441c/23177d5f6629268724e6e25a19047c3d3f65dc8d/README.yaml +++ b/Simulations/a7e/c6d/a7ec6ded506e2f92f704630d74da8d5d0bf9441c/23177d5f6629268724e6e25a19047c3d3f65dc8d/README.yaml @@ -56,9 +56,13 @@ WARNINGS: ORIENTATION: x-normal ID: 364 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/CHOL/CLA/SOD (73:10:9:9) bilayer at 310 K (Slipids, GROMACS, 600 ns) [NMRlipids simulation 364] + name: Molecular dynamics trajectory of a DPPC/CHOL/CLA/SOD (73:10:9:9) bilayer at + 310 K (Slipids, GROMACS, 600 ns) [NMRlipids simulation 364] alternateName: 392DPPC_52CHOL_17760SOL_48SOD_48CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 392 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 73 mol%), 52 CHOL (cholesterol, 10 mol%), 48 CLA (9 mol%) and 48 SOD (9 mol%) at 310 K. Simulated with Slipids in GROMACS for 600 ns (108184 atoms). Deposited as NMRlipids Databank simulation 364 and available from https://doi.org/10.5281/zenodo.3540513. + description: Molecular dynamics trajectory of a lipid bilayer of 392 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 73 mol%), 52 CHOL (cholesterol, 10 mol%), 48 CLA (9 mol%) and 48 SOD (9 mol%) + at 310 K. Simulated with Slipids in GROMACS for 600 ns (108184 atoms). Deposited + as NMRlipids Databank simulation 364 and available from https://doi.org/10.5281/zenodo.3540513. sameAs: https://doi.org/10.5281/zenodo.3540513 datePublished: '2019-11-13' license: diff --git a/Simulations/a7f/9f3/a7f9f36feaa77791483dadb0157f86a6a519f2c3/a30f01e8771c44dc59b78753d1dd27ca67920e38/README.yaml b/Simulations/a7f/9f3/a7f9f36feaa77791483dadb0157f86a6a519f2c3/a30f01e8771c44dc59b78753d1dd27ca67920e38/README.yaml index cec868b678..77b792a118 100644 --- a/Simulations/a7f/9f3/a7f9f36feaa77791483dadb0157f86a6a519f2c3/a30f01e8771c44dc59b78753d1dd27ca67920e38/README.yaml +++ b/Simulations/a7f/9f3/a7f9f36feaa77791483dadb0157f86a6a519f2c3/a30f01e8771c44dc59b78753d1dd27ca67920e38/README.yaml @@ -38,9 +38,12 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/1 ID: 828 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 300 K (Sage 2.2.1, GROMACS, 500 ns) [NMRlipids simulation 828] + name: Molecular dynamics trajectory of a POPC bilayer at 300 K (Sage 2.2.1, GROMACS, + 500 ns) [NMRlipids simulation 828] alternateName: POPCandTIP3P - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 300 K. Simulated with Sage 2.2.1 in GROMACS for 500 ns (32512 atoms). Deposited as NMRlipids Databank simulation 828 and available from https://doi.org/10.5281/zenodo.14713771. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 300 K. Simulated with Sage 2.2.1 in GROMACS for 500 ns (32512 atoms). Deposited + as NMRlipids Databank simulation 828 and available from https://doi.org/10.5281/zenodo.14713771. sameAs: https://doi.org/10.5281/zenodo.14713771 datePublished: '2025-01-21' license: diff --git a/Simulations/a7f/b85/a7fb85d6b732ed89d397a399a6e48394643c615e/58cb99b06261921c135b2cdc21b7da242943819b/README.yaml b/Simulations/a7f/b85/a7fb85d6b732ed89d397a399a6e48394643c615e/58cb99b06261921c135b2cdc21b7da242943819b/README.yaml index 14aec783c6..e5ef227005 100644 --- a/Simulations/a7f/b85/a7fb85d6b732ed89d397a399a6e48394643c615e/58cb99b06261921c135b2cdc21b7da242943819b/README.yaml +++ b/Simulations/a7f/b85/a7fb85d6b732ed89d397a399a6e48394643c615e/58cb99b06261921c135b2cdc21b7da242943819b/README.yaml @@ -44,9 +44,12 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/1 ID: 696 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 298.15 K (Slipids, GROMACS 2021, 1001 ns) [NMRlipids simulation 696] + name: Molecular dynamics trajectory of a POPC bilayer at 298.15 K (Slipids, GROMACS + 2021, 1001 ns) [NMRlipids simulation 696] alternateName: Slipids_POPC_L - description: Molecular dynamics trajectory of a lipid bilayer of 1024 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 298.15 K. Simulated with Slipids in GROMACS 2021 for 1001 ns (290816 atoms). Deposited as NMRlipids Databank simulation 696 and available from https://doi.org/10.5281/zenodo.7022749. + description: Molecular dynamics trajectory of a lipid bilayer of 1024 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 298.15 K. Simulated with Slipids in GROMACS 2021 for 1001 ns (290816 atoms). + Deposited as NMRlipids Databank simulation 696 and available from https://doi.org/10.5281/zenodo.7022749. sameAs: https://doi.org/10.5281/zenodo.7022749 datePublished: '2022-08-23' license: diff --git a/Simulations/a83/8a3/a838a3b62e4ff9edf29f2013d35d7574ffba80d9/fa399e3ef1f309213768537b89f7811ccbe5f1fc/README.yaml b/Simulations/a83/8a3/a838a3b62e4ff9edf29f2013d35d7574ffba80d9/fa399e3ef1f309213768537b89f7811ccbe5f1fc/README.yaml index d742b959ae..923602da29 100644 --- a/Simulations/a83/8a3/a838a3b62e4ff9edf29f2013d35d7574ffba80d9/fa399e3ef1f309213768537b89f7811ccbe5f1fc/README.yaml +++ b/Simulations/a83/8a3/a838a3b62e4ff9edf29f2013d35d7574ffba80d9/fa399e3ef1f309213768537b89f7811ccbe5f1fc/README.yaml @@ -87,9 +87,16 @@ EXPERIMENT: GM1: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPE/SOD/CHOL/CLA/SM16/POPS/GM1 (28:18:17:15:10:7:4:3) bilayer at 300 K (Charmm36, GROMACS 2020.4, 300 ns) [NMRlipids simulation 767] + name: Molecular dynamics trajectory of a POPC/POPE/SOD/CHOL/CLA/SM16/POPS/GM1 (28:18:17:15:10:7:4:3) + bilayer at 300 K (Charmm36, GROMACS 2020.4, 300 ns) [NMRlipids simulation 767] alternateName: POPC_POPE_POPS_SM_CHOL_GM1_NaCL - description: Molecular dynamics trajectory of a lipid bilayer of 152 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 28 mol%), 96 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 18 mol%), 92 SOD (17 mol%), 80 CHOL (cholesterol, 15 mol%), 56 CLA (10 mol%), 36 SM16 (N-palmitoyl-D-erythro-sphingosylphosphorylcholine, 7 mol%), 20 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 4 mol%) and 16 GM1 (GM1(d18:1/16:0), 3 mol%) at 300 K. Simulated with Charmm36 in GROMACS 2020.4 for 300 ns (107288 atoms). Deposited as NMRlipids Databank simulation 767 and available from https://doi.org/10.5281/zenodo.8331752. + description: Molecular dynamics trajectory of a lipid bilayer of 152 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 28 mol%), 96 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 18 mol%), + 92 SOD (17 mol%), 80 CHOL (cholesterol, 15 mol%), 56 CLA (10 mol%), 36 SM16 (N-palmitoyl-D-erythro-sphingosylphosphorylcholine, + 7 mol%), 20 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 4 mol%) + and 16 GM1 (GM1(d18:1/16:0), 3 mol%) at 300 K. Simulated with Charmm36 in GROMACS + 2020.4 for 300 ns (107288 atoms). Deposited as NMRlipids Databank simulation 767 + and available from https://doi.org/10.5281/zenodo.8331752. sameAs: https://doi.org/10.5281/zenodo.8331752 datePublished: '2023-09-10' license: @@ -184,7 +191,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.8331752 identifier: 10.5281/zenodo.8331752 url: https://doi.org/10.5281/zenodo.8331752 - name: MD simulation trajectory for Heterogenous lipid bilayer with 150mM NaCl concentration + name: MD simulation trajectory for Heterogenous lipid bilayer with 150mM NaCl + concentration publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/a83/e44/a83e446866beb4a5e1e267bb24e5544f97b7219c/af8a05f5ae6178825d417dfef0197fcb823796ff/README.yaml b/Simulations/a83/e44/a83e446866beb4a5e1e267bb24e5544f97b7219c/af8a05f5ae6178825d417dfef0197fcb823796ff/README.yaml index d844ed6571..8aed4c85e1 100644 --- a/Simulations/a83/e44/a83e446866beb4a5e1e267bb24e5544f97b7219c/af8a05f5ae6178825d417dfef0197fcb823796ff/README.yaml +++ b/Simulations/a83/e44/a83e446866beb4a5e1e267bb24e5544f97b7219c/af8a05f5ae6178825d417dfef0197fcb823796ff/README.yaml @@ -48,9 +48,12 @@ EXPERIMENT: - 10.1021/jp511159q/1 ID: 400 bioschema_properties: - name: Molecular dynamics trajectory of a POPE bilayer at 310 K (GROMOS-CKP, GROMACS 2018.3, 100 ns) [NMRlipids simulation 400] + name: Molecular dynamics trajectory of a POPE bilayer at 310 K (GROMOS-CKP, GROMACS + 2018.3, 100 ns) [NMRlipids simulation 400] alternateName: 500POPE_25000SOL_310K_GROMOS-CKP - description: Molecular dynamics trajectory of a lipid bilayer of 500 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) at 310 K. Simulated with GROMOS-CKP in GROMACS 2018.3 for 100 ns (101000 atoms). Deposited as NMRlipids Databank simulation 400 and available from https://doi.org/10.5281/zenodo.3237754. + description: Molecular dynamics trajectory of a lipid bilayer of 500 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) + at 310 K. Simulated with GROMOS-CKP in GROMACS 2018.3 for 100 ns (101000 atoms). + Deposited as NMRlipids Databank simulation 400 and available from https://doi.org/10.5281/zenodo.3237754. sameAs: https://doi.org/10.5281/zenodo.3237754 datePublished: '2019-06-03' license: diff --git a/Simulations/a8c/902/a8c902af83267fc386b4222715cf64fffbb3468f/fd8a26805af5559d5a75fd4965ae9ba24b831005/README.yaml b/Simulations/a8c/902/a8c902af83267fc386b4222715cf64fffbb3468f/fd8a26805af5559d5a75fd4965ae9ba24b831005/README.yaml index aa08c210f9..5acf61f504 100644 --- a/Simulations/a8c/902/a8c902af83267fc386b4222715cf64fffbb3468f/fd8a26805af5559d5a75fd4965ae9ba24b831005/README.yaml +++ b/Simulations/a8c/902/a8c902af83267fc386b4222715cf64fffbb3468f/fd8a26805af5559d5a75fd4965ae9ba24b831005/README.yaml @@ -43,9 +43,12 @@ EXPERIMENT: DRPC: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a DRPC bilayer at 333.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 635] + name: Molecular dynamics trajectory of a DRPC bilayer at 333.15 K (CHARMM36, GROMACS, + 1001 ns) [NMRlipids simulation 635] alternateName: 64DRPC_3200SOL_333K - description: Molecular dynamics trajectory of a lipid bilayer of 64 DRPC (1,2-(14:1$^\Delta9$)-sn-glycero-3-phosphocholine) at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (16896 atoms). Deposited as NMRlipids Databank simulation 635 and available from https://doi.org/10.5281/zenodo.6943413. + description: Molecular dynamics trajectory of a lipid bilayer of 64 DRPC (1,2-(14:1$^\Delta9$)-sn-glycero-3-phosphocholine) + at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (16896 atoms). Deposited + as NMRlipids Databank simulation 635 and available from https://doi.org/10.5281/zenodo.6943413. sameAs: https://doi.org/10.5281/zenodo.6943413 datePublished: '2022-07-30' license: @@ -133,7 +136,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.6943413 identifier: 10.5281/zenodo.6943413 url: https://doi.org/10.5281/zenodo.6943413 - name: Simulations of different single-component bilayers, three different system sizes + name: Simulations of different single-component bilayers, three different system + sizes publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/a92/c4f/a92c4f19b6fbeb659e51814d66c94e0b0d09b3af/b0e5132128bf4152704a2575833b1a05650527d6/README.yaml b/Simulations/a92/c4f/a92c4f19b6fbeb659e51814d66c94e0b0d09b3af/b0e5132128bf4152704a2575833b1a05650527d6/README.yaml index 71e71635e2..41db43acb8 100644 --- a/Simulations/a92/c4f/a92c4f19b6fbeb659e51814d66c94e0b0d09b3af/b0e5132128bf4152704a2575833b1a05650527d6/README.yaml +++ b/Simulations/a92/c4f/a92c4f19b6fbeb659e51814d66c94e0b0d09b3af/b0e5132128bf4152704a2575833b1a05650527d6/README.yaml @@ -49,9 +49,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/3 ID: 697 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (89:11) bilayer at 298.15 K (Slipids, GROMACS 2021, 1001 ns) [NMRlipids simulation 697] + name: Molecular dynamics trajectory of a POPC/CHOL (89:11) bilayer at 298.15 K (Slipids, + GROMACS 2021, 1001 ns) [NMRlipids simulation 697] alternateName: Slipids_POPC_CHOL11_L - description: Molecular dynamics trajectory of a lipid bilayer of 1024 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 89 mol%) and 128 CHOL (cholesterol, 11 mol%) at 298.15 K. Simulated with Slipids in GROMACS 2021 for 1001 ns (319488 atoms). Deposited as NMRlipids Databank simulation 697 and available from https://doi.org/10.5281/zenodo.7022749. + description: Molecular dynamics trajectory of a lipid bilayer of 1024 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 89 mol%) and 128 CHOL (cholesterol, 11 mol%) at 298.15 K. Simulated with Slipids + in GROMACS 2021 for 1001 ns (319488 atoms). Deposited as NMRlipids Databank simulation + 697 and available from https://doi.org/10.5281/zenodo.7022749. sameAs: https://doi.org/10.5281/zenodo.7022749 datePublished: '2022-08-23' license: diff --git a/Simulations/a95/28e/a9528e5501b2b41af2dd6f8540cb514a3eb186e0/5e86893c5c58e183eca1082084085205569a596b/DPPC_FragmentQuality.json b/Simulations/a95/28e/a9528e5501b2b41af2dd6f8540cb514a3eb186e0/5e86893c5c58e183eca1082084085205569a596b/DPPC_FragmentQuality.json new file mode 100644 index 0000000000..3b2248a10c --- /dev/null +++ b/Simulations/a95/28e/a9528e5501b2b41af2dd6f8540cb514a3eb186e0/5e86893c5c58e183eca1082084085205569a596b/DPPC_FragmentQuality.json @@ -0,0 +1 @@ +{"sn-1": NaN, "sn-2": NaN, "headgroup": 0.6585, "total": 0.6585} \ No newline at end of file diff --git a/Simulations/a95/28e/a9528e5501b2b41af2dd6f8540cb514a3eb186e0/5e86893c5c58e183eca1082084085205569a596b/DPPC_OrderParameters_quality.json b/Simulations/a95/28e/a9528e5501b2b41af2dd6f8540cb514a3eb186e0/5e86893c5c58e183eca1082084085205569a596b/DPPC_OrderParameters_quality.json new file mode 100644 index 0000000000..c36dfedf79 --- /dev/null +++ b/Simulations/a95/28e/a9528e5501b2b41af2dd6f8540cb514a3eb186e0/5e86893c5c58e183eca1082084085205569a596b/DPPC_OrderParameters_quality.json @@ -0,0 +1,84 @@ +{ + "10.1021/bi00687a021/1": { + "M_G1C10_M M_G1C10H1_M": NaN, + "M_G1C10_M M_G1C10H2_M": NaN, + "M_G1C11_M M_G1C11H1_M": NaN, + "M_G1C11_M M_G1C11H2_M": NaN, + "M_G1C12_M M_G1C12H1_M": NaN, + "M_G1C12_M M_G1C12H2_M": NaN, + "M_G1C13_M M_G1C13H1_M": NaN, + "M_G1C13_M M_G1C13H2_M": NaN, + "M_G1C14_M M_G1C14H1_M": NaN, + "M_G1C14_M M_G1C14H2_M": NaN, + "M_G1C15_M M_G1C15H1_M": NaN, + "M_G1C15_M M_G1C15H2_M": NaN, + "M_G1C16_M M_G1C16H1_M": NaN, + "M_G1C16_M M_G1C16H2_M": NaN, + "M_G1C17_M M_G1C17H1_M": NaN, + "M_G1C17_M M_G1C17H2_M": NaN, + "M_G1C17_M M_G1C17H3_M": NaN, + "M_G1C3_M M_G1C3H1_M": NaN, + "M_G1C3_M M_G1C3H2_M": NaN, + "M_G1C4_M M_G1C4H1_M": NaN, + "M_G1C4_M M_G1C4H2_M": NaN, + "M_G1C5_M M_G1C5H1_M": NaN, + "M_G1C5_M M_G1C5H2_M": NaN, + "M_G1C6_M M_G1C6H1_M": NaN, + "M_G1C6_M M_G1C6H2_M": NaN, + "M_G1C7_M M_G1C7H1_M": NaN, + "M_G1C7_M M_G1C7H2_M": NaN, + "M_G1C8_M M_G1C8H1_M": NaN, + "M_G1C8_M M_G1C8H2_M": NaN, + "M_G1C9_M M_G1C9H1_M": NaN, + "M_G1C9_M M_G1C9H2_M": NaN, + "M_G1_M M_G1H1_M": NaN, + "M_G1_M M_G1H2_M": NaN, + "M_G2C10_M M_G2C10H1_M": NaN, + "M_G2C10_M M_G2C10H2_M": NaN, + "M_G2C11_M M_G2C11H1_M": NaN, + "M_G2C11_M M_G2C11H2_M": NaN, + "M_G2C12_M M_G2C12H1_M": NaN, + "M_G2C12_M M_G2C12H2_M": NaN, + "M_G2C13_M M_G2C13H1_M": NaN, + "M_G2C13_M M_G2C13H2_M": NaN, + "M_G2C14_M M_G2C14H1_M": NaN, + "M_G2C14_M M_G2C14H2_M": NaN, + "M_G2C15_M M_G2C15H1_M": NaN, + "M_G2C15_M M_G2C15H2_M": NaN, + "M_G2C16_M M_G2C16H1_M": NaN, + "M_G2C16_M M_G2C16H2_M": NaN, + "M_G2C17_M M_G2C17H1_M": NaN, + "M_G2C17_M M_G2C17H2_M": NaN, + "M_G2C17_M M_G2C17H3_M": NaN, + "M_G2C3_M M_G2C3H1_M": NaN, + "M_G2C3_M M_G2C3H2_M": NaN, + "M_G2C4_M M_G2C4H1_M": NaN, + "M_G2C4_M M_G2C4H2_M": NaN, + "M_G2C5_M M_G2C5H1_M": NaN, + "M_G2C5_M M_G2C5H2_M": NaN, + "M_G2C6_M M_G2C6H1_M": NaN, + "M_G2C6_M M_G2C6H2_M": NaN, + "M_G2C7_M M_G2C7H1_M": NaN, + "M_G2C7_M M_G2C7H2_M": NaN, + "M_G2C8_M M_G2C8H1_M": NaN, + "M_G2C8_M M_G2C8H2_M": NaN, + "M_G2C9_M M_G2C9H1_M": NaN, + "M_G2C9_M M_G2C9H2_M": NaN, + "M_G2_M M_G2H1_M": NaN, + "M_G3C4_M M_G3C4H1_M": 0.0311, + "M_G3C4_M M_G3C4H2_M": 0.028, + "M_G3C5_M M_G3C5H1_M": 0.9378, + "M_G3C5_M M_G3C5H2_M": 0.9612, + "M_G3N6C1_M M_G3N6C1H1_M": 0.9891, + "M_G3N6C1_M M_G3N6C1H2_M": 0.9885, + "M_G3N6C1_M M_G3N6C1H3_M": 0.9889, + "M_G3N6C2_M M_G3N6C2H1_M": 0.9896, + "M_G3N6C2_M M_G3N6C2H2_M": 0.9888, + "M_G3N6C2_M M_G3N6C2H3_M": 0.9882, + "M_G3N6C3_M M_G3N6C3H1_M": 0.9888, + "M_G3N6C3_M M_G3N6C3H2_M": 0.9875, + "M_G3N6C3_M M_G3N6C3H3_M": 0.9891, + "M_G3_M M_G3H1_M": 0.0252, + "M_G3_M M_G3H2_M": 0.9707 + } +} \ No newline at end of file diff --git a/Simulations/a95/28e/a9528e5501b2b41af2dd6f8540cb514a3eb186e0/5e86893c5c58e183eca1082084085205569a596b/FormFactorQuality.json b/Simulations/a95/28e/a9528e5501b2b41af2dd6f8540cb514a3eb186e0/5e86893c5c58e183eca1082084085205569a596b/FormFactorQuality.json new file mode 100644 index 0000000000..2b998799cf --- /dev/null +++ b/Simulations/a95/28e/a9528e5501b2b41af2dd6f8540cb514a3eb186e0/5e86893c5c58e183eca1082084085205569a596b/FormFactorQuality.json @@ -0,0 +1 @@ +[0.4525, 92.7955] \ No newline at end of file diff --git a/Simulations/a95/28e/a9528e5501b2b41af2dd6f8540cb514a3eb186e0/5e86893c5c58e183eca1082084085205569a596b/README.yaml b/Simulations/a95/28e/a9528e5501b2b41af2dd6f8540cb514a3eb186e0/5e86893c5c58e183eca1082084085205569a596b/README.yaml index 5a00c9c2fa..f2c7df8725 100644 --- a/Simulations/a95/28e/a9528e5501b2b41af2dd6f8540cb514a3eb186e0/5e86893c5c58e183eca1082084085205569a596b/README.yaml +++ b/Simulations/a95/28e/a9528e5501b2b41af2dd6f8540cb514a3eb186e0/5e86893c5c58e183eca1082084085205569a596b/README.yaml @@ -39,3 +39,9 @@ NUMBER_OF_ATOMS: 53000 DATEOFRUNNING: 15/09/2026 TYPEOFSYSTEM: lipid bilayer ID: 935 +EXPERIMENT: + ORDERPARAMETER: + DPPC: + - 10.1021/bi00687a021/1 + FORMFACTOR: + - 10.1016/j.bbamem.2011.07.022/4 diff --git a/Simulations/a95/28e/a9528e5501b2b41af2dd6f8540cb514a3eb186e0/5e86893c5c58e183eca1082084085205569a596b/SYSTEM_quality.json b/Simulations/a95/28e/a9528e5501b2b41af2dd6f8540cb514a3eb186e0/5e86893c5c58e183eca1082084085205569a596b/SYSTEM_quality.json new file mode 100644 index 0000000000..b09389b199 --- /dev/null +++ b/Simulations/a95/28e/a9528e5501b2b41af2dd6f8540cb514a3eb186e0/5e86893c5c58e183eca1082084085205569a596b/SYSTEM_quality.json @@ -0,0 +1 @@ +{"headgroup": 0.6585, "tails": 0.0, "total": 0.6585} \ No newline at end of file diff --git a/Simulations/aa4/aec/aa4aec0dbfa357ebbf08f7ddd67add35eed59fbf/69991d6f6724d5557ed6b7801ae6ead2a76348c0/README.yaml b/Simulations/aa4/aec/aa4aec0dbfa357ebbf08f7ddd67add35eed59fbf/69991d6f6724d5557ed6b7801ae6ead2a76348c0/README.yaml index 2b83890a66..296f924c4a 100644 --- a/Simulations/aa4/aec/aa4aec0dbfa357ebbf08f7ddd67add35eed59fbf/69991d6f6724d5557ed6b7801ae6ead2a76348c0/README.yaml +++ b/Simulations/aa4/aec/aa4aec0dbfa357ebbf08f7ddd67add35eed59fbf/69991d6f6724d5557ed6b7801ae6ead2a76348c0/README.yaml @@ -57,9 +57,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 139 bioschema_properties: - name: Molecular dynamics trajectory of a POPE/POPG/SOD (60:20:20) bilayer at 310 K (GROMOS-CKP, GROMACS 2018.3, 100 ns) [NMRlipids simulation 139] + name: Molecular dynamics trajectory of a POPE/POPG/SOD (60:20:20) bilayer at 310 + K (GROMOS-CKP, GROMACS 2018.3, 100 ns) [NMRlipids simulation 139] alternateName: 126POPG_374POPE_25000SOL_126SOD_310K_GROMOS-CKP - description: Molecular dynamics trajectory of a lipid bilayer of 374 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 60 mol%), 126 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 20 mol%) and 126 SOD (20 mol%) at 310 K. Simulated with GROMOS-CKP in GROMACS 2018.3 for 100 ns (101252 atoms). Deposited as NMRlipids Databank simulation 139 and available from https://doi.org/10.5281/zenodo.3266238. + description: Molecular dynamics trajectory of a lipid bilayer of 374 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, + 60 mol%), 126 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 20 mol%) + and 126 SOD (20 mol%) at 310 K. Simulated with GROMOS-CKP in GROMACS 2018.3 for + 100 ns (101252 atoms). Deposited as NMRlipids Databank simulation 139 and available + from https://doi.org/10.5281/zenodo.3266238. sameAs: https://doi.org/10.5281/zenodo.3266238 datePublished: '2019-07-02' license: diff --git a/Simulations/aa4/e17/aa4e17293e2aecd83d08cb841a8c748446f9d597/0d7032928ab1b626803550c7a23196c612b4430f/README.yaml b/Simulations/aa4/e17/aa4e17293e2aecd83d08cb841a8c748446f9d597/0d7032928ab1b626803550c7a23196c612b4430f/README.yaml index c88aaf337d..b6cf4e5913 100644 --- a/Simulations/aa4/e17/aa4e17293e2aecd83d08cb841a8c748446f9d597/0d7032928ab1b626803550c7a23196c612b4430f/README.yaml +++ b/Simulations/aa4/e17/aa4e17293e2aecd83d08cb841a8c748446f9d597/0d7032928ab1b626803550c7a23196c612b4430f/README.yaml @@ -53,9 +53,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 138 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPG/SOD (54:23:23) bilayer at 310 K (Slipids, GROMACS 2018.3, 100 ns) [NMRlipids simulation 138] + name: Molecular dynamics trajectory of a POPC/POPG/SOD (54:23:23) bilayer at 310 + K (Slipids, GROMACS 2018.3, 100 ns) [NMRlipids simulation 138] alternateName: 150POPG_350POPC_25000SOL_150SOD_310K - description: Molecular dynamics trajectory of a lipid bilayer of 350 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 54 mol%), 150 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 23 mol%) and 150 SOD (23 mol%) at 310 K. Simulated with Slipids in GROMACS 2018.3 for 100 ns (141100 atoms). Deposited as NMRlipids Databank simulation 138 and available from https://doi.org/10.5281/zenodo.3240156. + description: Molecular dynamics trajectory of a lipid bilayer of 350 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 54 mol%), 150 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 23 mol%) + and 150 SOD (23 mol%) at 310 K. Simulated with Slipids in GROMACS 2018.3 for 100 + ns (141100 atoms). Deposited as NMRlipids Databank simulation 138 and available + from https://doi.org/10.5281/zenodo.3240156. sameAs: https://doi.org/10.5281/zenodo.3240156 datePublished: '2019-06-06' license: diff --git a/Simulations/aa7/50c/aa750ccdf3c44dfa6c4ca794d20e43dde4576d59/c77ba6a9f03254a9b798f1805477bcadd4984fc8/README.yaml b/Simulations/aa7/50c/aa750ccdf3c44dfa6c4ca794d20e43dde4576d59/c77ba6a9f03254a9b798f1805477bcadd4984fc8/README.yaml index 3cbdf1c86e..c17d83663e 100644 --- a/Simulations/aa7/50c/aa750ccdf3c44dfa6c4ca794d20e43dde4576d59/c77ba6a9f03254a9b798f1805477bcadd4984fc8/README.yaml +++ b/Simulations/aa7/50c/aa750ccdf3c44dfa6c4ca794d20e43dde4576d59/c77ba6a9f03254a9b798f1805477bcadd4984fc8/README.yaml @@ -47,9 +47,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 167 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (84:8:8) bilayer at 298 K (MacRog, GROMACS 4.5, 50 ns) [NMRlipids simulation 167] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (84:8:8) bilayer at 298 K + (MacRog, GROMACS 4.5, 50 ns) [NMRlipids simulation 167] alternateName: 288POPC_14554SOL_27SOD_27CLA_298K - description: Molecular dynamics trajectory of a lipid bilayer of 288 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 84 mol%), 27 CLA (8 mol%) and 27 SOD (8 mol%) at 298 K. Simulated with MacRog in GROMACS 4.5 for 50 ns (82308 atoms). Deposited as NMRlipids Databank simulation 167 and available from https://doi.org/10.5281/zenodo.14976. + description: Molecular dynamics trajectory of a lipid bilayer of 288 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 84 mol%), 27 CLA (8 mol%) and 27 SOD (8 mol%) at 298 K. Simulated with MacRog + in GROMACS 4.5 for 50 ns (82308 atoms). Deposited as NMRlipids Databank simulation + 167 and available from https://doi.org/10.5281/zenodo.14976. sameAs: https://doi.org/10.5281/zenodo.14976 datePublished: '2015-02-10' license: diff --git a/Simulations/aa8/3d4/aa83d427cf495177dfceb987c21d57388f98b79f/b32c12316d8452925a2e9009c0e3c48732fd40ef/README.yaml b/Simulations/aa8/3d4/aa83d427cf495177dfceb987c21d57388f98b79f/b32c12316d8452925a2e9009c0e3c48732fd40ef/README.yaml index bba82f2be0..7a789f3dd7 100644 --- a/Simulations/aa8/3d4/aa83d427cf495177dfceb987c21d57388f98b79f/b32c12316d8452925a2e9009c0e3c48732fd40ef/README.yaml +++ b/Simulations/aa8/3d4/aa83d427cf495177dfceb987c21d57388f98b79f/b32c12316d8452925a2e9009c0e3c48732fd40ef/README.yaml @@ -45,9 +45,13 @@ WARNINGS: PBC: z-jumps ID: 100 bioschema_properties: - name: Molecular dynamics trajectory of a DOPS/SOD (50:50) bilayer at 303 K (Slipids, GROMACS 5.0.4, 50 ns) [NMRlipids simulation 100] + name: Molecular dynamics trajectory of a DOPS/SOD (50:50) bilayer at 303 K (Slipids, + GROMACS 5.0.4, 50 ns) [NMRlipids simulation 100] alternateName: 288DOPS_11232SOL_288SOD_303K - description: Molecular dynamics trajectory of a lipid bilayer of 288 DOPS (1,2-dioleoyl-sn-glycero-3-phospho-L-serine, 50 mol%) and 288 SOD (50 mol%) at 303 K. Simulated with Slipids in GROMACS 5.0.4 for 50 ns (71712 atoms). Deposited as NMRlipids Databank simulation 100 and available from https://doi.org/10.5281/zenodo.495510. + description: Molecular dynamics trajectory of a lipid bilayer of 288 DOPS (1,2-dioleoyl-sn-glycero-3-phospho-L-serine, + 50 mol%) and 288 SOD (50 mol%) at 303 K. Simulated with Slipids in GROMACS 5.0.4 + for 50 ns (71712 atoms). Deposited as NMRlipids Databank simulation 100 and available + from https://doi.org/10.5281/zenodo.495510. sameAs: https://doi.org/10.5281/zenodo.495510 datePublished: '2017-04-07' license: @@ -135,7 +139,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.495510 identifier: 10.5281/zenodo.495510 url: https://doi.org/10.5281/zenodo.495510 - name: 'Md Simulation Trajectory Of A Fully Hydrated Dops Bilayer: Slipids, Gromacs 5.0.4. 2017.' + name: 'Md Simulation Trajectory Of A Fully Hydrated Dops Bilayer: Slipids, Gromacs + 5.0.4. 2017.' publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/ab4/a4c/ab4a4cd981f07a5634e982ee57e3534e413a8946/704f4f55c4c4ca03a355d1a640101442f088d0b7/README.yaml b/Simulations/ab4/a4c/ab4a4cd981f07a5634e982ee57e3534e413a8946/704f4f55c4c4ca03a355d1a640101442f088d0b7/README.yaml index d927399325..7535670e5f 100644 --- a/Simulations/ab4/a4c/ab4a4cd981f07a5634e982ee57e3534e413a8946/704f4f55c4c4ca03a355d1a640101442f088d0b7/README.yaml +++ b/Simulations/ab4/a4c/ab4a4cd981f07a5634e982ee57e3534e413a8946/704f4f55c4c4ca03a355d1a640101442f088d0b7/README.yaml @@ -46,9 +46,12 @@ EXPERIMENT: - 10.1016/j.bbamem.2011.07.022/4 ID: 593 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC bilayer at 323 K (Poger GROMOS 53A6_L, GROMACS 4.0.7, 100 ns) [NMRlipids simulation 593] + name: Molecular dynamics trajectory of a DPPC bilayer at 323 K (Poger GROMOS 53A6_L, + GROMACS 4.0.7, 100 ns) [NMRlipids simulation 593] alternateName: 128DPPC_5841SOL_323K - description: Molecular dynamics trajectory of a lipid bilayer of 128 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) at 323 K. Simulated with Poger GROMOS 53A6_L in GROMACS 4.0.7 for 100 ns (23923 atoms). Deposited as NMRlipids Databank simulation 593 and available from https://doi.org/10.5281/zenodo.14595. + description: Molecular dynamics trajectory of a lipid bilayer of 128 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) + at 323 K. Simulated with Poger GROMOS 53A6_L in GROMACS 4.0.7 for 100 ns (23923 + atoms). Deposited as NMRlipids Databank simulation 593 and available from https://doi.org/10.5281/zenodo.14595. sameAs: https://doi.org/10.5281/zenodo.14595 datePublished: '2015-01-27' license: @@ -140,7 +143,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.14595 identifier: 10.5281/zenodo.14595 url: https://doi.org/10.5281/zenodo.14595 - name: Md Simulation Trajectory And Related Files For Dppc Bilayer In Full Hydration (Poger Gromos 53A6_L, Gromacs 4.0.7, Pme, Traj 2) + name: Md Simulation Trajectory And Related Files For Dppc Bilayer In Full Hydration + (Poger Gromos 53A6_L, Gromacs 4.0.7, Pme, Traj 2) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/ab5/b66/ab5b667604e840d8fbb48739c2d42eb6c12c0608/9b8e5f299caa6a5b03e56ad6a9991739394d709c/README.yaml b/Simulations/ab5/b66/ab5b667604e840d8fbb48739c2d42eb6c12c0608/9b8e5f299caa6a5b03e56ad6a9991739394d709c/README.yaml index f91ae865d6..d1623ac2a4 100644 --- a/Simulations/ab5/b66/ab5b667604e840d8fbb48739c2d42eb6c12c0608/9b8e5f299caa6a5b03e56ad6a9991739394d709c/README.yaml +++ b/Simulations/ab5/b66/ab5b667604e840d8fbb48739c2d42eb6c12c0608/9b8e5f299caa6a5b03e56ad6a9991739394d709c/README.yaml @@ -55,9 +55,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 55 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/CLA/SOD/CHOL (74:9:9:9) bilayer at 305 K (Slipids, GROMACS, 1000 ns) [NMRlipids simulation 55] + name: Molecular dynamics trajectory of a DPPC/CLA/SOD/CHOL (74:9:9:9) bilayer at + 305 K (Slipids, GROMACS, 1000 ns) [NMRlipids simulation 55] alternateName: 1032DPPC_120CHOL_46440SOL_124SOD_124CLA_305K - description: Molecular dynamics trajectory of a lipid bilayer of 1032 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 74 mol%), 124 CLA (9 mol%), 124 SOD (9 mol%) and 120 CHOL (cholesterol, 9 mol%) at 305 K. Simulated with Slipids in GROMACS for 1000 ns (282608 atoms). Deposited as NMRlipids Databank simulation 55 and available from https://doi.org/10.5281/zenodo.3539263. + description: Molecular dynamics trajectory of a lipid bilayer of 1032 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 74 mol%), 124 CLA (9 mol%), 124 SOD (9 mol%) and 120 CHOL (cholesterol, 9 mol%) + at 305 K. Simulated with Slipids in GROMACS for 1000 ns (282608 atoms). Deposited + as NMRlipids Databank simulation 55 and available from https://doi.org/10.5281/zenodo.3539263. sameAs: https://doi.org/10.5281/zenodo.3539263 datePublished: '2019-11-12' license: diff --git a/Simulations/ac0/992/ac0992c74e87361fbbfcc9e64507b5de2ffd6b12/2bae4180a38766f03b70977d1a998b5cfe290f4a/README.yaml b/Simulations/ac0/992/ac0992c74e87361fbbfcc9e64507b5de2ffd6b12/2bae4180a38766f03b70977d1a998b5cfe290f4a/README.yaml index 412b22560a..18fc05027e 100644 --- a/Simulations/ac0/992/ac0992c74e87361fbbfcc9e64507b5de2ffd6b12/2bae4180a38766f03b70977d1a998b5cfe290f4a/README.yaml +++ b/Simulations/ac0/992/ac0992c74e87361fbbfcc9e64507b5de2ffd6b12/2bae4180a38766f03b70977d1a998b5cfe290f4a/README.yaml @@ -60,9 +60,16 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 618 bioschema_properties: - name: Molecular dynamics trajectory of a CLA/POPC/CAL/POPS/SOD (41:27:21:5:5) bilayer at 320 K (CHARMM36 with NBFIX for calcium ions, GROMACS 2018.6, 437 ns) [NMRlipids simulation 618] + name: Molecular dynamics trajectory of a CLA/POPC/CAL/POPS/SOD (41:27:21:5:5) bilayer + at 320 K (CHARMM36 with NBFIX for calcium ions, GROMACS 2018.6, 437 ns) [NMRlipids + simulation 618] alternateName: 250POPC_50POPS_11174SOL_50SOD_189CAL_378CLA_320K - description: Molecular dynamics trajectory of a lipid bilayer of 378 CLA (41 mol%), 250 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 27 mol%), 189 CAL (21 mol%), 50 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 5 mol%) and 50 SOD (5 mol%) at 320 K. Simulated with CHARMM36 with NBFIX for calcium ions in GROMACS 2018.6 for 437 ns (73989 atoms). Deposited as NMRlipids Databank simulation 618 and available from https://doi.org/10.5281/zenodo.3371327. + description: Molecular dynamics trajectory of a lipid bilayer of 378 CLA (41 mol%), + 250 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 27 mol%), 189 CAL + (21 mol%), 50 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 5 mol%) + and 50 SOD (5 mol%) at 320 K. Simulated with CHARMM36 with NBFIX for calcium ions + in GROMACS 2018.6 for 437 ns (73989 atoms). Deposited as NMRlipids Databank simulation + 618 and available from https://doi.org/10.5281/zenodo.3371327. sameAs: https://doi.org/10.5281/zenodo.3371327 datePublished: '2019-08-19' license: diff --git a/Simulations/ac2/651/ac265157c0b640f701dacff0f46c2eb25392b4a3/386a224988e3b7a2fe053b893ebc601111027dd4/README.yaml b/Simulations/ac2/651/ac265157c0b640f701dacff0f46c2eb25392b4a3/386a224988e3b7a2fe053b893ebc601111027dd4/README.yaml index 510d2153b1..9b3459defb 100644 --- a/Simulations/ac2/651/ac265157c0b640f701dacff0f46c2eb25392b4a3/386a224988e3b7a2fe053b893ebc601111027dd4/README.yaml +++ b/Simulations/ac2/651/ac265157c0b640f701dacff0f46c2eb25392b4a3/386a224988e3b7a2fe053b893ebc601111027dd4/README.yaml @@ -49,9 +49,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 542 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/CLA/SOD (82:9:9) bilayer at 300 K (Slipids, GROMACS 4.6, 500 ns) [NMRlipids simulation 542] + name: Molecular dynamics trajectory of a DPPC/CLA/SOD (82:9:9) bilayer at 300 K + (Slipids, GROMACS 4.6, 500 ns) [NMRlipids simulation 542] alternateName: 1152DPPC_46440SOL_124SOD_124CLA_300K - description: Molecular dynamics trajectory of a lipid bilayer of 1152 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 82 mol%), 124 CLA (9 mol%) and 124 SOD (9 mol%) at 300 K. Simulated with Slipids in GROMACS 4.6 for 500 ns (289328 atoms). Deposited as NMRlipids Databank simulation 542 and available from https://doi.org/10.5281/zenodo.439080. + description: Molecular dynamics trajectory of a lipid bilayer of 1152 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 82 mol%), 124 CLA (9 mol%) and 124 SOD (9 mol%) at 300 K. Simulated with Slipids + in GROMACS 4.6 for 500 ns (289328 atoms). Deposited as NMRlipids Databank simulation + 542 and available from https://doi.org/10.5281/zenodo.439080. sameAs: https://doi.org/10.5281/zenodo.439080 datePublished: '2017-03-29' license: @@ -143,7 +147,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.439080 identifier: 10.5281/zenodo.439080 url: https://doi.org/10.5281/zenodo.439080 - name: Simulations Of Dppc/Cholesterol Bilayers With The Slipids Force Field, Part 2/2 + name: Simulations Of Dppc/Cholesterol Bilayers With The Slipids Force Field, Part + 2/2 publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/ac4/242/ac4242b5de6414ba1746a497c552dd92472a1ce3/5e793f635d83d27ec6aff19ad4eb688a872a9d76/README.yaml b/Simulations/ac4/242/ac4242b5de6414ba1746a497c552dd92472a1ce3/5e793f635d83d27ec6aff19ad4eb688a872a9d76/README.yaml index 454b009008..9dd7d58978 100644 --- a/Simulations/ac4/242/ac4242b5de6414ba1746a497c552dd92472a1ce3/5e793f635d83d27ec6aff19ad4eb688a872a9d76/README.yaml +++ b/Simulations/ac4/242/ac4242b5de6414ba1746a497c552dd92472a1ce3/5e793f635d83d27ec6aff19ad4eb688a872a9d76/README.yaml @@ -47,9 +47,12 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/1 ID: 422 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 298 K (Chiu Gromos, GROMACS 4.5, 50 ns) [NMRlipids simulation 422] + name: Molecular dynamics trajectory of a POPC bilayer at 298 K (Chiu Gromos, GROMACS + 4.5, 50 ns) [NMRlipids simulation 422] alternateName: 128POPC_3552SOL_298K - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 298 K. Simulated with Chiu Gromos in GROMACS 4.5 for 50 ns (17312 atoms). Deposited as NMRlipids Databank simulation 422 and available from https://doi.org/10.5281/zenodo.6656031. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 298 K. Simulated with Chiu Gromos in GROMACS 4.5 for 50 ns (17312 atoms). Deposited + as NMRlipids Databank simulation 422 and available from https://doi.org/10.5281/zenodo.6656031. sameAs: https://doi.org/10.5281/zenodo.6656031 datePublished: '2015-02-20' license: @@ -142,7 +145,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.6656031 identifier: 10.5281/zenodo.6656031 url: https://doi.org/10.5281/zenodo.6656031 - name: MD simulation trajectory and related files for POPC bilayer (Chiu et al. Gromos version, Gromacs 4.5) + name: MD simulation trajectory and related files for POPC bilayer (Chiu et al. + Gromos version, Gromacs 4.5) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/ac5/b6c/ac5b6ccff03b63ef8911fc59da61a453cf8b91bd/39682d6f1bd5d4a75b00099ccd42cfdb71c1a730/README.yaml b/Simulations/ac5/b6c/ac5b6ccff03b63ef8911fc59da61a453cf8b91bd/39682d6f1bd5d4a75b00099ccd42cfdb71c1a730/README.yaml index 13c326895d..b2ab386447 100644 --- a/Simulations/ac5/b6c/ac5b6ccff03b63ef8911fc59da61a453cf8b91bd/39682d6f1bd5d4a75b00099ccd42cfdb71c1a730/README.yaml +++ b/Simulations/ac5/b6c/ac5b6ccff03b63ef8911fc59da61a453cf8b91bd/39682d6f1bd5d4a75b00099ccd42cfdb71c1a730/README.yaml @@ -52,9 +52,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 190 bioschema_properties: - name: Molecular dynamics trajectory of a POPE/CLA/SOD (83:8:8) bilayer at 310 K (GROMOS-CKP, GROMACS 5.1.2, 100 ns) [NMRlipids simulation 190] + name: Molecular dynamics trajectory of a POPE/CLA/SOD (83:8:8) bilayer at 310 K + (GROMOS-CKP, GROMACS 5.1.2, 100 ns) [NMRlipids simulation 190] alternateName: 500POPE_25000SOL_50SOD_50CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 500 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 83 mol%), 50 CLA (8 mol%) and 50 SOD (8 mol%) at 310 K. Simulated with GROMOS-CKP in GROMACS 5.1.2 for 100 ns (101100 atoms). Deposited as NMRlipids Databank simulation 190 and available from https://doi.org/10.5281/zenodo.2574491. + description: Molecular dynamics trajectory of a lipid bilayer of 500 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, + 83 mol%), 50 CLA (8 mol%) and 50 SOD (8 mol%) at 310 K. Simulated with GROMOS-CKP + in GROMACS 5.1.2 for 100 ns (101100 atoms). Deposited as NMRlipids Databank simulation + 190 and available from https://doi.org/10.5281/zenodo.2574491. sameAs: https://doi.org/10.5281/zenodo.2574491 datePublished: '2019-02-26' license: diff --git a/Simulations/ac7/4af/ac74afe8ad9307efcde1b91549950c33f4651572/f0d5b8342f3bd53ccb933806591012e78a43190a/README.yaml b/Simulations/ac7/4af/ac74afe8ad9307efcde1b91549950c33f4651572/f0d5b8342f3bd53ccb933806591012e78a43190a/README.yaml index 0bd639bbc2..62046f71fa 100644 --- a/Simulations/ac7/4af/ac74afe8ad9307efcde1b91549950c33f4651572/f0d5b8342f3bd53ccb933806591012e78a43190a/README.yaml +++ b/Simulations/ac7/4af/ac74afe8ad9307efcde1b91549950c33f4651572/f0d5b8342f3bd53ccb933806591012e78a43190a/README.yaml @@ -39,9 +39,13 @@ EXPERIMENT: C20: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/C20 (86:14) bilayer at 333 K (SLIPIDS, GROMACS, 100 ns) [NMRlipids simulation 888] + name: Molecular dynamics trajectory of a DPPC/C20 (86:14) bilayer at 333 K (SLIPIDS, + GROMACS, 100 ns) [NMRlipids simulation 888] alternateName: DPPC/C20 - description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 86 mol%) and 12 C20 (n-Eicosane, 14 mol%) at 333 K. Simulated with SLIPIDS in GROMACS for 100 ns (13563 atoms). Deposited as NMRlipids Databank simulation 888 and available from https://doi.org/10.5281/zenodo.7572990. + description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 86 mol%) and 12 C20 (n-Eicosane, 14 mol%) at 333 K. Simulated with SLIPIDS in + GROMACS for 100 ns (13563 atoms). Deposited as NMRlipids Databank simulation 888 + and available from https://doi.org/10.5281/zenodo.7572990. sameAs: https://doi.org/10.5281/zenodo.7572990 datePublished: '2023-01-26' license: @@ -133,7 +137,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.7572990 identifier: 10.5281/zenodo.7572990 url: https://doi.org/10.5281/zenodo.7572990 - name: 'MD simulation input files and results for ,,Atomistic MD simulations of n-alkanes in a phospholipid bilayer: CHARMM36 versus Slipids"' + name: 'MD simulation input files and results for ,,Atomistic MD simulations of + n-alkanes in a phospholipid bilayer: CHARMM36 versus Slipids"' publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/ade/d58/aded58ab5c0d40bf4651cb0a2f404ec7ef2be418/17cae4c7bb00a969a9bb45ee0ea074344e0190c9/README.yaml b/Simulations/ade/d58/aded58ab5c0d40bf4651cb0a2f404ec7ef2be418/17cae4c7bb00a969a9bb45ee0ea074344e0190c9/README.yaml index d3b550b6b7..fa7944d73b 100644 --- a/Simulations/ade/d58/aded58ab5c0d40bf4651cb0a2f404ec7ef2be418/17cae4c7bb00a969a9bb45ee0ea074344e0190c9/README.yaml +++ b/Simulations/ade/d58/aded58ab5c0d40bf4651cb0a2f404ec7ef2be418/17cae4c7bb00a969a9bb45ee0ea074344e0190c9/README.yaml @@ -41,9 +41,13 @@ EXPERIMENT: C20: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/C20 (86:14) bilayer at 333 K (CHARMM36, GROMACS, 100 ns) [NMRlipids simulation 887] + name: Molecular dynamics trajectory of a DPPC/C20 (86:14) bilayer at 333 K (CHARMM36, + GROMACS, 100 ns) [NMRlipids simulation 887] alternateName: DPPC/C20 - description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 86 mol%) and 12 C20 (n-Eicosane, 14 mol%) at 333 K. Simulated with CHARMM36 in GROMACS for 100 ns (13563 atoms). Deposited as NMRlipids Databank simulation 887 and available from https://doi.org/10.5281/zenodo.7572990. + description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 86 mol%) and 12 C20 (n-Eicosane, 14 mol%) at 333 K. Simulated with CHARMM36 in + GROMACS for 100 ns (13563 atoms). Deposited as NMRlipids Databank simulation 887 + and available from https://doi.org/10.5281/zenodo.7572990. sameAs: https://doi.org/10.5281/zenodo.7572990 datePublished: '2023-01-26' license: @@ -136,7 +140,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.7572990 identifier: 10.5281/zenodo.7572990 url: https://doi.org/10.5281/zenodo.7572990 - name: 'MD simulation input files and results for ,,Atomistic MD simulations of n-alkanes in a phospholipid bilayer: CHARMM36 versus Slipids"' + name: 'MD simulation input files and results for ,,Atomistic MD simulations of + n-alkanes in a phospholipid bilayer: CHARMM36 versus Slipids"' publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/ade/d58/aded58ab5c0d40bf4651cb0a2f404ec7ef2be418/9bffff4ec0adf428ee343f40f7322181cba1fa5a/README.yaml b/Simulations/ade/d58/aded58ab5c0d40bf4651cb0a2f404ec7ef2be418/9bffff4ec0adf428ee343f40f7322181cba1fa5a/README.yaml index c04cb4d344..1af4b9884f 100644 --- a/Simulations/ade/d58/aded58ab5c0d40bf4651cb0a2f404ec7ef2be418/9bffff4ec0adf428ee343f40f7322181cba1fa5a/README.yaml +++ b/Simulations/ade/d58/aded58ab5c0d40bf4651cb0a2f404ec7ef2be418/9bffff4ec0adf428ee343f40f7322181cba1fa5a/README.yaml @@ -42,9 +42,13 @@ EXPERIMENT: C20: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/C20 (86:14) bilayer at 333 K (CHARMM36, GROMACS 2018.7, 100 ns) [NMRlipids simulation 755] + name: Molecular dynamics trajectory of a DPPC/C20 (86:14) bilayer at 333 K (CHARMM36, + GROMACS 2018.7, 100 ns) [NMRlipids simulation 755] alternateName: DPPC:C20(72:12)_T333K - description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 86 mol%) and 12 C20 (n-Eicosane, 14 mol%) at 333 K. Simulated with CHARMM36 in GROMACS 2018.7 for 100 ns (13563 atoms). Deposited as NMRlipids Databank simulation 755 and available from https://doi.org/10.5281/zenodo.7572990. + description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 86 mol%) and 12 C20 (n-Eicosane, 14 mol%) at 333 K. Simulated with CHARMM36 in + GROMACS 2018.7 for 100 ns (13563 atoms). Deposited as NMRlipids Databank simulation + 755 and available from https://doi.org/10.5281/zenodo.7572990. sameAs: https://doi.org/10.5281/zenodo.7572990 datePublished: '2023-01-26' license: @@ -136,7 +140,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.7572990 identifier: 10.5281/zenodo.7572990 url: https://doi.org/10.5281/zenodo.7572990 - name: 'MD simulation input files and results for ,,Atomistic MD simulations of n-alkanes in a phospholipid bilayer: CHARMM36 versus Slipids"' + name: 'MD simulation input files and results for ,,Atomistic MD simulations of + n-alkanes in a phospholipid bilayer: CHARMM36 versus Slipids"' publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/aea/e9f/aeae9f138e796f374682a4d9ce4c1dd9f683aae8/0b2019438bdbdbb889227d8c6028ff7854561a26/README.yaml b/Simulations/aea/e9f/aeae9f138e796f374682a4d9ce4c1dd9f683aae8/0b2019438bdbdbb889227d8c6028ff7854561a26/README.yaml index 3653768f5e..4dd7f8ba5e 100644 --- a/Simulations/aea/e9f/aeae9f138e796f374682a4d9ce4c1dd9f683aae8/0b2019438bdbdbb889227d8c6028ff7854561a26/README.yaml +++ b/Simulations/aea/e9f/aeae9f138e796f374682a4d9ce4c1dd9f683aae8/0b2019438bdbdbb889227d8c6028ff7854561a26/README.yaml @@ -54,9 +54,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 270 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/CLA/SOD (41:29:29) bilayer at 323 K (OPLSAA-compatible Berger-DPPC-06, GROMACS 5.0.4, 120 ns) [NMRlipids simulation 270] + name: Molecular dynamics trajectory of a DPPC/CLA/SOD (41:29:29) bilayer at 323 + K (OPLSAA-compatible Berger-DPPC-06, GROMACS 5.0.4, 120 ns) [NMRlipids simulation + 270] alternateName: 72DPPC_2778SOL_51SOD_51CLA_323K - description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 41 mol%), 51 CLA (29 mol%) and 51 SOD (29 mol%) at 323 K. Simulated with OPLSAA-compatible Berger-DPPC-06 in GROMACS 5.0.4 for 120 ns (12036 atoms). Deposited as NMRlipids Databank simulation 270 and available from https://doi.org/10.5281/zenodo.17209. + description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 41 mol%), 51 CLA (29 mol%) and 51 SOD (29 mol%) at 323 K. Simulated with OPLSAA-compatible + Berger-DPPC-06 in GROMACS 5.0.4 for 120 ns (12036 atoms). Deposited as NMRlipids + Databank simulation 270 and available from https://doi.org/10.5281/zenodo.17209. sameAs: https://doi.org/10.5281/zenodo.17209 datePublished: '2015-04-28' license: diff --git a/Simulations/aeb/5b8/aeb5b8ead640deb6f88b14f3ce2bbdec07188ea9/7841befda427cfb4864d22adcba99c0f8a90e292/README.yaml b/Simulations/aeb/5b8/aeb5b8ead640deb6f88b14f3ce2bbdec07188ea9/7841befda427cfb4864d22adcba99c0f8a90e292/README.yaml index eb0402ece9..f040c48c5c 100644 --- a/Simulations/aeb/5b8/aeb5b8ead640deb6f88b14f3ce2bbdec07188ea9/7841befda427cfb4864d22adcba99c0f8a90e292/README.yaml +++ b/Simulations/aeb/5b8/aeb5b8ead640deb6f88b14f3ce2bbdec07188ea9/7841befda427cfb4864d22adcba99c0f8a90e292/README.yaml @@ -53,9 +53,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 518 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/DHMDMAB (64:18:18) bilayer at 313 K (Lipid14, GROMACS, 80 ns) [NMRlipids simulation 518] + name: Molecular dynamics trajectory of a POPC/CLA/DHMDMAB (64:18:18) bilayer at + 313 K (Lipid14, GROMACS, 80 ns) [NMRlipids simulation 518] alternateName: 100POPC_28DHMDMAB_6214SOL_28CLA_313K - description: Molecular dynamics trajectory of a lipid bilayer of 100 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 64 mol%), 28 CLA (18 mol%) and 28 DHMDMAB (dihexadecyldimethylammonium, 18 mol%) at 313 K. Simulated with Lipid14 in GROMACS for 80 ns (35066 atoms). Deposited as NMRlipids Databank simulation 518 and available from https://doi.org/10.5281/zenodo.1020593. + description: Molecular dynamics trajectory of a lipid bilayer of 100 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 64 mol%), 28 CLA (18 mol%) and 28 DHMDMAB (dihexadecyldimethylammonium, 18 mol%) + at 313 K. Simulated with Lipid14 in GROMACS for 80 ns (35066 atoms). Deposited + as NMRlipids Databank simulation 518 and available from https://doi.org/10.5281/zenodo.1020593. sameAs: https://doi.org/10.5281/zenodo.1020593 datePublished: '2017-10-18' license: @@ -144,7 +148,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1020593 identifier: 10.5281/zenodo.1020593 url: https://doi.org/10.5281/zenodo.1020593 - name: Popc Bilayer With 20% Of Dihexadecyldimethylammonium Simulated At T313K With The Lipid14 Model Using Gromacs + name: Popc Bilayer With 20% Of Dihexadecyldimethylammonium Simulated At T313K + With The Lipid14 Model Using Gromacs publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/aec/8cf/aec8cf3207aa4ab9efa02f7c3dce44997050f5ab/71a7aceda6cae85e8b582d6abbd78bfe5c999d91/README.yaml b/Simulations/aec/8cf/aec8cf3207aa4ab9efa02f7c3dce44997050f5ab/71a7aceda6cae85e8b582d6abbd78bfe5c999d91/README.yaml index df62fbb61a..cd853cf56f 100644 --- a/Simulations/aec/8cf/aec8cf3207aa4ab9efa02f7c3dce44997050f5ab/71a7aceda6cae85e8b582d6abbd78bfe5c999d91/README.yaml +++ b/Simulations/aec/8cf/aec8cf3207aa4ab9efa02f7c3dce44997050f5ab/71a7aceda6cae85e8b582d6abbd78bfe5c999d91/README.yaml @@ -39,9 +39,12 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/1 ID: 833 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 300 K (FF-development, GROMACS, 339 ns) [NMRlipids simulation 833] + name: Molecular dynamics trajectory of a POPC bilayer at 300 K (FF-development, + GROMACS, 339 ns) [NMRlipids simulation 833] alternateName: POPCandTIP3P - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 300 K. Simulated with FF-development in GROMACS for 339 ns (32512 atoms). Deposited as NMRlipids Databank simulation 833 and available from https://doi.org/10.5281/zenodo.15002801. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 300 K. Simulated with FF-development in GROMACS for 339 ns (32512 atoms). Deposited + as NMRlipids Databank simulation 833 and available from https://doi.org/10.5281/zenodo.15002801. sameAs: https://doi.org/10.5281/zenodo.15002801 datePublished: '2025-03-10' license: diff --git a/Simulations/aef/442/aef4429d5c23dd3d6aea0683a552c7d8cbc787df/03c4667949377aca6116c541ee3a7a26c367d8eb/README.yaml b/Simulations/aef/442/aef4429d5c23dd3d6aea0683a552c7d8cbc787df/03c4667949377aca6116c541ee3a7a26c367d8eb/README.yaml index c4ecc7c15d..ba40a2f2fa 100644 --- a/Simulations/aef/442/aef4429d5c23dd3d6aea0683a552c7d8cbc787df/03c4667949377aca6116c541ee3a7a26c367d8eb/README.yaml +++ b/Simulations/aef/442/aef4429d5c23dd3d6aea0683a552c7d8cbc787df/03c4667949377aca6116c541ee3a7a26c367d8eb/README.yaml @@ -45,9 +45,12 @@ EXPERIMENT: - 10.1021/jp511159q/1 ID: 790 bioschema_properties: - name: Molecular dynamics trajectory of a POPE bilayer at 310 K (Charmm36, GROMACS 2022.5, 512 ns) [NMRlipids simulation 790] + name: Molecular dynamics trajectory of a POPE bilayer at 310 K (Charmm36, GROMACS + 2022.5, 512 ns) [NMRlipids simulation 790] alternateName: POPE(313K,rfz) - description: Molecular dynamics trajectory of a lipid bilayer of 144 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) at 310 K. Simulated with Charmm36 in GROMACS 2022.5 for 512 ns (35280 atoms). Deposited as NMRlipids Databank simulation 790 and available from https://doi.org/10.5281/zenodo.8435138. + description: Molecular dynamics trajectory of a lipid bilayer of 144 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) + at 310 K. Simulated with Charmm36 in GROMACS 2022.5 for 512 ns (35280 atoms). + Deposited as NMRlipids Databank simulation 790 and available from https://doi.org/10.5281/zenodo.8435138. sameAs: https://doi.org/10.5281/zenodo.8435138 datePublished: '2023-10-12' license: diff --git a/Simulations/af2/1da/af21da6438fb2e1305dec6ef0a69e6148f11edfd/fdcab103936e99ce9736c2edca9650d783f466bc/README.yaml b/Simulations/af2/1da/af21da6438fb2e1305dec6ef0a69e6148f11edfd/fdcab103936e99ce9736c2edca9650d783f466bc/README.yaml index 9572edd4e0..c4a841a7d4 100644 --- a/Simulations/af2/1da/af21da6438fb2e1305dec6ef0a69e6148f11edfd/fdcab103936e99ce9736c2edca9650d783f466bc/README.yaml +++ b/Simulations/af2/1da/af21da6438fb2e1305dec6ef0a69e6148f11edfd/fdcab103936e99ce9736c2edca9650d783f466bc/README.yaml @@ -50,9 +50,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/8 ID: 698 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (62:38) bilayer at 298.15 K (MacRog, GROMACS 2021, 1001 ns) [NMRlipids simulation 698] + name: Molecular dynamics trajectory of a POPC/CHOL (62:38) bilayer at 298.15 K (MacRog, + GROMACS 2021, 1001 ns) [NMRlipids simulation 698] alternateName: MacRog_POPC_CHOL38_L - description: Molecular dynamics trajectory of a lipid bilayer of 1024 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 62 mol%) and 640 CHOL (cholesterol, 38 mol%) at 298.15 K. Simulated with MacRog in GROMACS 2021 for 1001 ns (434176 atoms). Deposited as NMRlipids Databank simulation 698 and available from https://doi.org/10.5281/zenodo.7061800. + description: Molecular dynamics trajectory of a lipid bilayer of 1024 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 62 mol%) and 640 CHOL (cholesterol, 38 mol%) at 298.15 K. Simulated with MacRog + in GROMACS 2021 for 1001 ns (434176 atoms). Deposited as NMRlipids Databank simulation + 698 and available from https://doi.org/10.5281/zenodo.7061800. sameAs: https://doi.org/10.5281/zenodo.7061800 datePublished: '2022-09-08' license: diff --git a/Simulations/af5/2bc/af52bc8271982d3d2a26ffe1a30028a3a72272f3/f4f170580e987fea0b9d73c6e239941d3f346f73/README.yaml b/Simulations/af5/2bc/af52bc8271982d3d2a26ffe1a30028a3a72272f3/f4f170580e987fea0b9d73c6e239941d3f346f73/README.yaml index 37ee8486d4..c4430020a7 100644 --- a/Simulations/af5/2bc/af52bc8271982d3d2a26ffe1a30028a3a72272f3/f4f170580e987fea0b9d73c6e239941d3f346f73/README.yaml +++ b/Simulations/af5/2bc/af52bc8271982d3d2a26ffe1a30028a3a72272f3/f4f170580e987fea0b9d73c6e239941d3f346f73/README.yaml @@ -51,9 +51,13 @@ EXPERIMENT: CHOL: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a SDPE/CHOL/DOG (58:33:9) bilayer at 310 K (Lipid17, GROMACS 18.7, 1000 ns) [NMRlipids simulation 721] + name: Molecular dynamics trajectory of a SDPE/CHOL/DOG (58:33:9) bilayer at 310 + K (Lipid17, GROMACS 18.7, 1000 ns) [NMRlipids simulation 721] alternateName: DOGandCHOLinSDPEwithLipid17 - description: Molecular dynamics trajectory of a lipid bilayer of 74 SDPE (1-stearoyl-2-docosahexaenoyl-sn-glycero-3-phosphoethanolamine, 58 mol%), 42 CHOL (cholesterol, 33 mol%) and 12 DOG (1,2-dioleoyl-sn-glycerol, 9 mol%) at 310 K. Simulated with Lipid17 in GROMACS 18.7 for 1000 ns (33542 atoms). Deposited as NMRlipids Databank simulation 721 and available from https://doi.org/10.5281/zenodo.6823118. + description: Molecular dynamics trajectory of a lipid bilayer of 74 SDPE (1-stearoyl-2-docosahexaenoyl-sn-glycero-3-phosphoethanolamine, + 58 mol%), 42 CHOL (cholesterol, 33 mol%) and 12 DOG (1,2-dioleoyl-sn-glycerol, + 9 mol%) at 310 K. Simulated with Lipid17 in GROMACS 18.7 for 1000 ns (33542 atoms). + Deposited as NMRlipids Databank simulation 721 and available from https://doi.org/10.5281/zenodo.6823118. sameAs: https://doi.org/10.5281/zenodo.6823118 datePublished: '2022-07-12' license: diff --git a/Simulations/afa/b24/afab24a3270f4289a86544d8f6e9b3bd72395d3e/5b4aadb79ec3804f4ca138b684e1cc23d7e3833b/README.yaml b/Simulations/afa/b24/afab24a3270f4289a86544d8f6e9b3bd72395d3e/5b4aadb79ec3804f4ca138b684e1cc23d7e3833b/README.yaml index b11461602d..12d928d699 100644 --- a/Simulations/afa/b24/afab24a3270f4289a86544d8f6e9b3bd72395d3e/5b4aadb79ec3804f4ca138b684e1cc23d7e3833b/README.yaml +++ b/Simulations/afa/b24/afab24a3270f4289a86544d8f6e9b3bd72395d3e/5b4aadb79ec3804f4ca138b684e1cc23d7e3833b/README.yaml @@ -48,9 +48,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 436 bioschema_properties: - name: Molecular dynamics trajectory of a DOPS/SOD (50:50) bilayer at 303 K (Berger, GROMACS, 100 ns) [NMRlipids simulation 436] + name: Molecular dynamics trajectory of a DOPS/SOD (50:50) bilayer at 303 K (Berger, + GROMACS, 100 ns) [NMRlipids simulation 436] alternateName: 128DOPS_4480SOL_128SOD_303K_v1 - description: Molecular dynamics trajectory of a lipid bilayer of 128 DOPS (1,2-dioleoyl-sn-glycero-3-phospho-L-serine, 50 mol%) and 128 SOD (50 mol%) at 303 K. Simulated with Berger in GROMACS for 100 ns (20864 atoms). Deposited as NMRlipids Databank simulation 436 and available from https://doi.org/10.5281/zenodo.1129419. + description: Molecular dynamics trajectory of a lipid bilayer of 128 DOPS (1,2-dioleoyl-sn-glycero-3-phospho-L-serine, + 50 mol%) and 128 SOD (50 mol%) at 303 K. Simulated with Berger in GROMACS for + 100 ns (20864 atoms). Deposited as NMRlipids Databank simulation 436 and available + from https://doi.org/10.5281/zenodo.1129419. sameAs: https://doi.org/10.5281/zenodo.1129419 datePublished: '2017-12-24' license: diff --git a/Simulations/afd/10f/afd10f4a726ac10fab788e3ceb067156edda533a/b2038b0680c733660e8f1894d0c0ddfe711d6f28/README.yaml b/Simulations/afd/10f/afd10f4a726ac10fab788e3ceb067156edda533a/b2038b0680c733660e8f1894d0c0ddfe711d6f28/README.yaml index ebd38fdbd9..b23075ea0a 100644 --- a/Simulations/afd/10f/afd10f4a726ac10fab788e3ceb067156edda533a/b2038b0680c733660e8f1894d0c0ddfe711d6f28/README.yaml +++ b/Simulations/afd/10f/afd10f4a726ac10fab788e3ceb067156edda533a/b2038b0680c733660e8f1894d0c0ddfe711d6f28/README.yaml @@ -38,9 +38,12 @@ EXPERIMENT: FORMFACTOR: - 10.1016/j.bbamem.2011.07.022/7 bioschema_properties: - name: Molecular dynamics trajectory of a DLPC bilayer at 303 K (CHARMM36/LJ-PME, GROMACS Gromacs 2022, 100 ns) [NMRlipids simulation 914] + name: Molecular dynamics trajectory of a DLPC bilayer at 303 K (CHARMM36/LJ-PME, + GROMACS Gromacs 2022, 100 ns) [NMRlipids simulation 914] alternateName: Fully hydrated DLPC bilayer in SPC/E water (LJ-PME) - description: Molecular dynamics trajectory of a lipid bilayer of 100 DLPC (1,2-dilauroyl-sn-glycero-3-phosphocholine) at 303 K. Simulated with CHARMM36/LJ-PME in GROMACS Gromacs 2022 for 100 ns (23542 atoms). Deposited as NMRlipids Databank simulation 914 and available from https://doi.org/10.5281/zenodo.20579050. + description: Molecular dynamics trajectory of a lipid bilayer of 100 DLPC (1,2-dilauroyl-sn-glycero-3-phosphocholine) + at 303 K. Simulated with CHARMM36/LJ-PME in GROMACS Gromacs 2022 for 100 ns (23542 + atoms). Deposited as NMRlipids Databank simulation 914 and available from https://doi.org/10.5281/zenodo.20579050. sameAs: https://doi.org/10.5281/zenodo.20579050 datePublished: '2026-06-07' license: @@ -131,7 +134,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.20579050 identifier: 10.5281/zenodo.20579050 url: https://doi.org/10.5281/zenodo.20579050 - name: Fully hydrated DLPC bilayer at different temperatures simulated using CHARMM36 with LJ-PME and LJ-cutoff + name: Fully hydrated DLPC bilayer at different temperatures simulated using CHARMM36 + with LJ-PME and LJ-cutoff publisher: Zenodo _source: api: datacite diff --git a/Simulations/b02/d72/b02d72fcc1d55c526bf127e43ec88ba9f6eb2e0e/2b72f2e8f583393c9fb84f2b7c248ffa0c87a6cd/README.yaml b/Simulations/b02/d72/b02d72fcc1d55c526bf127e43ec88ba9f6eb2e0e/2b72f2e8f583393c9fb84f2b7c248ffa0c87a6cd/README.yaml index d9412df956..c7b1dffe8f 100644 --- a/Simulations/b02/d72/b02d72fcc1d55c526bf127e43ec88ba9f6eb2e0e/2b72f2e8f583393c9fb84f2b7c248ffa0c87a6cd/README.yaml +++ b/Simulations/b02/d72/b02d72fcc1d55c526bf127e43ec88ba9f6eb2e0e/2b72f2e8f583393c9fb84f2b7c248ffa0c87a6cd/README.yaml @@ -54,9 +54,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 79 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (60:27:13) bilayer at 313 K (ECC-lipids, GROMACS 5.1.4, 300 ns) [NMRlipids simulation 79] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (60:27:13) bilayer at 313 + K (ECC-lipids, GROMACS 5.1.4, 300 ns) [NMRlipids simulation 79] alternateName: 128POPC_6400SOL_29CAL_58CLA_313K_OPC4model - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 60 mol%), 58 CLA (27 mol%) and 29 CAL (13 mol%) at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 300 ns (42839 atoms). Deposited as NMRlipids Databank simulation 79 and available from https://doi.org/10.5281/zenodo.1118980. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 60 mol%), 58 CLA (27 mol%) and 29 CAL (13 mol%) at 313 K. Simulated with ECC-lipids + in GROMACS 5.1.4 for 300 ns (42839 atoms). Deposited as NMRlipids Databank simulation + 79 and available from https://doi.org/10.5281/zenodo.1118980. sameAs: https://doi.org/10.5281/zenodo.1118980 datePublished: '2017-12-19' license: @@ -146,7 +150,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1118980 identifier: 10.5281/zenodo.1118980 url: https://doi.org/10.5281/zenodo.1118980 - name: Simulations Of Popc Lipid Bilayer In Water Solution At Various Nacl And Cacl2 Concentrations Using Ecc-Popc Force Field And Various Water Models + name: Simulations Of Popc Lipid Bilayer In Water Solution At Various Nacl And + Cacl2 Concentrations Using Ecc-Popc Force Field And Various Water Models publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/b04/7ff/b047ffe7ca543800f5d13bc850bbb66924b7231b/76a77f734fea9fcca1189a8c5b4533a68d73ead5/README.yaml b/Simulations/b04/7ff/b047ffe7ca543800f5d13bc850bbb66924b7231b/76a77f734fea9fcca1189a8c5b4533a68d73ead5/README.yaml index eac885d951..d5f8838261 100644 --- a/Simulations/b04/7ff/b047ffe7ca543800f5d13bc850bbb66924b7231b/76a77f734fea9fcca1189a8c5b4533a68d73ead5/README.yaml +++ b/Simulations/b04/7ff/b047ffe7ca543800f5d13bc850bbb66924b7231b/76a77f734fea9fcca1189a8c5b4533a68d73ead5/README.yaml @@ -55,9 +55,14 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/7 ID: 206 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (66:34) bilayer at 298 K (Berger and Modified Höltje model for cholesterol, GROMACS 4.5, 50 ns) [NMRlipids simulation 206] + name: Molecular dynamics trajectory of a POPC/CHOL (66:34) bilayer at 298 K (Berger + and Modified Höltje model for cholesterol, GROMACS 4.5, 50 ns) [NMRlipids simulation + 206] alternateName: 44CHOL_84POPC_6794SOL_298K_Berger - description: Molecular dynamics trajectory of a lipid bilayer of 84 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 66 mol%) and 44 CHOL (cholesterol, 34 mol%) at 298 K. Simulated with Berger and Modified Höltje model for cholesterol in GROMACS 4.5 for 50 ns (26026 atoms). Deposited as NMRlipids Databank simulation 206 and available from https://doi.org/10.5281/zenodo.4643985. + description: Molecular dynamics trajectory of a lipid bilayer of 84 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 66 mol%) and 44 CHOL (cholesterol, 34 mol%) at 298 K. Simulated with Berger and + Modified Höltje model for cholesterol in GROMACS 4.5 for 50 ns (26026 atoms). + Deposited as NMRlipids Databank simulation 206 and available from https://doi.org/10.5281/zenodo.4643985. sameAs: https://doi.org/10.5281/zenodo.4643985 datePublished: '2014-12-17' license: @@ -153,7 +158,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.4643985 identifier: 10.5281/zenodo.4643985 url: https://doi.org/10.5281/zenodo.4643985 - name: MD simulation trajectory and related files for POPC/cholesterol (34 mol%) bilayer (Berger model delivered by Tieleman, modified Höltje, Gromacs 4.5) + name: MD simulation trajectory and related files for POPC/cholesterol (34 mol%) + bilayer (Berger model delivered by Tieleman, modified Höltje, Gromacs 4.5) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/b06/79c/b0679cd5bb4bed509b91a002305d2771ed4ad54e/72ec31258e95aefa0d053131b9e734b4b11eb030/README.yaml b/Simulations/b06/79c/b0679cd5bb4bed509b91a002305d2771ed4ad54e/72ec31258e95aefa0d053131b9e734b4b11eb030/README.yaml index 898cdebc73..a22acaa8ce 100644 --- a/Simulations/b06/79c/b0679cd5bb4bed509b91a002305d2771ed4ad54e/72ec31258e95aefa0d053131b9e734b4b11eb030/README.yaml +++ b/Simulations/b06/79c/b0679cd5bb4bed509b91a002305d2771ed4ad54e/72ec31258e95aefa0d053131b9e734b4b11eb030/README.yaml @@ -44,9 +44,12 @@ TOP: DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 497 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 298 K (Berger, GROMACS 4.5, 50 ns) [NMRlipids simulation 497] + name: Molecular dynamics trajectory of a POPC bilayer at 298 K (Berger, GROMACS + 4.5, 50 ns) [NMRlipids simulation 497] alternateName: POPC_T298K - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 298 K. Simulated with Berger in GROMACS 4.5 for 50 ns (28526 atoms). Deposited as NMRlipids Databank simulation 497 and available from https://doi.org/10.5281/zenodo.4643875. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 298 K. Simulated with Berger in GROMACS 4.5 for 50 ns (28526 atoms). Deposited + as NMRlipids Databank simulation 497 and available from https://doi.org/10.5281/zenodo.4643875. sameAs: https://doi.org/10.5281/zenodo.4643875 datePublished: '2014-12-17' license: @@ -141,7 +144,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.4643875 identifier: 10.5281/zenodo.4643875 url: https://doi.org/10.5281/zenodo.4643875 - name: MD simulation trajectory and related files for POPC bilayer (Berger model delivered by Tieleman, Gromacs 4.5) + name: MD simulation trajectory and related files for POPC bilayer (Berger model + delivered by Tieleman, Gromacs 4.5) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/b0a/582/b0a58233e19732457334067340fdb6a0549b123b/c73550b177a385ac49a36356193958687efdc3f5/README.yaml b/Simulations/b0a/582/b0a58233e19732457334067340fdb6a0549b123b/c73550b177a385ac49a36356193958687efdc3f5/README.yaml index 9a805a5d83..5da96086dc 100644 --- a/Simulations/b0a/582/b0a58233e19732457334067340fdb6a0549b123b/c73550b177a385ac49a36356193958687efdc3f5/README.yaml +++ b/Simulations/b0a/582/b0a58233e19732457334067340fdb6a0549b123b/c73550b177a385ac49a36356193958687efdc3f5/README.yaml @@ -54,9 +54,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 294 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPS/POT (67:17:17) bilayer at 298 K (ECC-lipids, SPC water model, ECC-ions, GROMACS 2018.0, 983 ns) [NMRlipids simulation 294] + name: Molecular dynamics trajectory of a POPC/POPS/POT (67:17:17) bilayer at 298 + K (ECC-lipids, SPC water model, ECC-ions, GROMACS 2018.0, 983 ns) [NMRlipids simulation + 294] alternateName: 12POPS_48POPC_3600SOL_12POT_298K_ECC-lipid - description: Molecular dynamics trajectory of a lipid bilayer of 48 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 67 mol%), 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 17 mol%) and 12 POT (17 mol%) at 298 K. Simulated with ECC-lipids, SPC water model, ECC-ions in GROMACS 2018.0 for 983 ns (18768 atoms). Deposited as NMRlipids Databank simulation 294 and available from https://doi.org/10.5281/zenodo.1488094. + description: Molecular dynamics trajectory of a lipid bilayer of 48 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 67 mol%), 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 17 mol%) + and 12 POT (17 mol%) at 298 K. Simulated with ECC-lipids, SPC water model, ECC-ions + in GROMACS 2018.0 for 983 ns (18768 atoms). Deposited as NMRlipids Databank simulation + 294 and available from https://doi.org/10.5281/zenodo.1488094. sameAs: https://doi.org/10.5281/zenodo.1488094 datePublished: '2018-11-14' license: @@ -147,7 +153,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1488094 identifier: 10.5281/zenodo.1488094 url: https://doi.org/10.5281/zenodo.1488094 - name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS (various mixtures) with ECC-lipids force field, and Na+ (K+) counterions + name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS + (various mixtures) with ECC-lipids force field, and Na+ (K+) counterions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/b16/7e2/b167e26f39a390c69bc605c2217f732d854c6395/f5de1720a24e1896cf96afc94fc4ef028adc47d0/README.yaml b/Simulations/b16/7e2/b167e26f39a390c69bc605c2217f732d854c6395/f5de1720a24e1896cf96afc94fc4ef028adc47d0/README.yaml index ab048e5104..853de6acba 100644 --- a/Simulations/b16/7e2/b167e26f39a390c69bc605c2217f732d854c6395/f5de1720a24e1896cf96afc94fc4ef028adc47d0/README.yaml +++ b/Simulations/b16/7e2/b167e26f39a390c69bc605c2217f732d854c6395/f5de1720a24e1896cf96afc94fc4ef028adc47d0/README.yaml @@ -55,9 +55,14 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/2 ID: 305 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (94:6) bilayer at 298 K (Berger and Modified Höltje model for cholesterol, GROMACS 4.5, 50 ns) [NMRlipids simulation 305] + name: Molecular dynamics trajectory of a POPC/CHOL (94:6) bilayer at 298 K (Berger + and Modified Höltje model for cholesterol, GROMACS 4.5, 50 ns) [NMRlipids simulation + 305] alternateName: 8CHOL_120POPC_7290SOL_298K_Berger - description: Molecular dynamics trajectory of a lipid bilayer of 120 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 94 mol%) and 8 CHOL (cholesterol, 6 mol%) at 298 K. Simulated with Berger and Modified Höltje model for cholesterol in GROMACS 4.5 for 50 ns (28342 atoms). Deposited as NMRlipids Databank simulation 305 and available from https://doi.org/10.5281/zenodo.4643899. + description: Molecular dynamics trajectory of a lipid bilayer of 120 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 94 mol%) and 8 CHOL (cholesterol, 6 mol%) at 298 K. Simulated with Berger and + Modified Höltje model for cholesterol in GROMACS 4.5 for 50 ns (28342 atoms). + Deposited as NMRlipids Databank simulation 305 and available from https://doi.org/10.5281/zenodo.4643899. sameAs: https://doi.org/10.5281/zenodo.4643899 datePublished: '2014-12-17' license: @@ -153,7 +158,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.4643899 identifier: 10.5281/zenodo.4643899 url: https://doi.org/10.5281/zenodo.4643899 - name: MD simulation trajectory and related files for POPC/cholesterol (7 mol%) bilayer (Berger model delivered by Tieleman, modified Höltje, Gromacs 4.5) + name: MD simulation trajectory and related files for POPC/cholesterol (7 mol%) + bilayer (Berger model delivered by Tieleman, modified Höltje, Gromacs 4.5) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/b1f/987/b1f9878b432b8834ab7089bb250e2608913c636e/205acffa603d25a3d5d72a6a5a33ef2952bf1643/README.yaml b/Simulations/b1f/987/b1f9878b432b8834ab7089bb250e2608913c636e/205acffa603d25a3d5d72a6a5a33ef2952bf1643/README.yaml index b6384dc074..dead5f8e8e 100644 --- a/Simulations/b1f/987/b1f9878b432b8834ab7089bb250e2608913c636e/205acffa603d25a3d5d72a6a5a33ef2952bf1643/README.yaml +++ b/Simulations/b1f/987/b1f9878b432b8834ab7089bb250e2608913c636e/205acffa603d25a3d5d72a6a5a33ef2952bf1643/README.yaml @@ -43,9 +43,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 520 bioschema_properties: - name: Molecular dynamics trajectory of a DOPC bilayer at 293.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 520] + name: Molecular dynamics trajectory of a DOPC bilayer at 293.15 K (CHARMM36, GROMACS, + 1001 ns) [NMRlipids simulation 520] alternateName: 64DOPC_3200SOL_293K - description: Molecular dynamics trajectory of a lipid bilayer of 64 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) at 293.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (18432 atoms). Deposited as NMRlipids Databank simulation 520 and available from https://doi.org/10.5281/zenodo.6943086. + description: Molecular dynamics trajectory of a lipid bilayer of 64 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) + at 293.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (18432 atoms). Deposited + as NMRlipids Databank simulation 520 and available from https://doi.org/10.5281/zenodo.6943086. sameAs: https://doi.org/10.5281/zenodo.6943086 datePublished: '2022-07-30' license: diff --git a/Simulations/b23/d28/b23d28fa4a500716f0af641a7b274ed74c0ed4af/e04e3b99e8e7fbce0a119c88df424c02eb6f2874/README.yaml b/Simulations/b23/d28/b23d28fa4a500716f0af641a7b274ed74c0ed4af/e04e3b99e8e7fbce0a119c88df424c02eb6f2874/README.yaml index a128f8c3ee..129c67fbf9 100644 --- a/Simulations/b23/d28/b23d28fa4a500716f0af641a7b274ed74c0ed4af/e04e3b99e8e7fbce0a119c88df424c02eb6f2874/README.yaml +++ b/Simulations/b23/d28/b23d28fa4a500716f0af641a7b274ed74c0ed4af/e04e3b99e8e7fbce0a119c88df424c02eb6f2874/README.yaml @@ -52,9 +52,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/9 ID: 699 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (53:47) bilayer at 298.15 K (MacRog, GROMACS 2021, 1001 ns) [NMRlipids simulation 699] + name: Molecular dynamics trajectory of a POPC/CHOL (53:47) bilayer at 298.15 K (MacRog, + GROMACS 2021, 1001 ns) [NMRlipids simulation 699] alternateName: MacRog_POPC_CHOL47_M - description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 53 mol%) and 224 CHOL (cholesterol, 47 mol%) at 298.15 K. Simulated with MacRog in GROMACS 2021 for 1001 ns (122880 atoms). Deposited as NMRlipids Databank simulation 699 and available from https://doi.org/10.5281/zenodo.7061800. + description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 53 mol%) and 224 CHOL (cholesterol, 47 mol%) at 298.15 K. Simulated with MacRog + in GROMACS 2021 for 1001 ns (122880 atoms). Deposited as NMRlipids Databank simulation + 699 and available from https://doi.org/10.5281/zenodo.7061800. sameAs: https://doi.org/10.5281/zenodo.7061800 datePublished: '2022-09-08' license: diff --git a/Simulations/b25/326/b253266e10dc4ba34ace7082a565507511b79446/444419368f25543b5ee3248af5345ceadfa11884/README.yaml b/Simulations/b25/326/b253266e10dc4ba34ace7082a565507511b79446/444419368f25543b5ee3248af5345ceadfa11884/README.yaml index a43c372423..4a68a4f89f 100644 --- a/Simulations/b25/326/b253266e10dc4ba34ace7082a565507511b79446/444419368f25543b5ee3248af5345ceadfa11884/README.yaml +++ b/Simulations/b25/326/b253266e10dc4ba34ace7082a565507511b79446/444419368f25543b5ee3248af5345ceadfa11884/README.yaml @@ -62,9 +62,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 424 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/POPS/SOD/CAL (56:15:11:11:7) bilayer at 298 K (Lipid17 and Dang ions, GROMACS 2018.0, 1000 ns) [NMRlipids simulation 424] + name: Molecular dynamics trajectory of a POPC/CLA/POPS/SOD/CAL (56:15:11:11:7) bilayer + at 298 K (Lipid17 and Dang ions, GROMACS 2018.0, 1000 ns) [NMRlipids simulation + 424] alternateName: 60POPC_12POPS_3561SOL_8CAL_16CLA_12SOD_298K - description: Molecular dynamics trajectory of a lipid bilayer of 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 56 mol%), 16 CLA (15 mol%), 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 11 mol%), 12 SOD (11 mol%) and 8 CAL (7 mol%) at 298 K. Simulated with Lipid17 and Dang ions in GROMACS 2018.0 for 1000 ns (20283 atoms). Deposited as NMRlipids Databank simulation 424 and available from https://doi.org/10.5281/zenodo.1487761. + description: Molecular dynamics trajectory of a lipid bilayer of 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 56 mol%), 16 CLA (15 mol%), 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, + 11 mol%), 12 SOD (11 mol%) and 8 CAL (7 mol%) at 298 K. Simulated with Lipid17 + and Dang ions in GROMACS 2018.0 for 1000 ns (20283 atoms). Deposited as NMRlipids + Databank simulation 424 and available from https://doi.org/10.5281/zenodo.1487761. sameAs: https://doi.org/10.5281/zenodo.1487761 datePublished: '2018-11-14' license: @@ -157,7 +163,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1487761 identifier: 10.5281/zenodo.1487761 url: https://doi.org/10.5281/zenodo.1487761 - name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS with the lipid17 force field, only counterions, and CaCl2 concentrations + name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS + with the lipid17 force field, only counterions, and CaCl2 concentrations publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/b26/a77/b26a77bb464996d420103059fbfc792f35f000d8/508b09dc91e254f859051b74040b1dc8e1342919/README.yaml b/Simulations/b26/a77/b26a77bb464996d420103059fbfc792f35f000d8/508b09dc91e254f859051b74040b1dc8e1342919/README.yaml index b3ae41e0c5..f2a0b9d27e 100644 --- a/Simulations/b26/a77/b26a77bb464996d420103059fbfc792f35f000d8/508b09dc91e254f859051b74040b1dc8e1342919/README.yaml +++ b/Simulations/b26/a77/b26a77bb464996d420103059fbfc792f35f000d8/508b09dc91e254f859051b74040b1dc8e1342919/README.yaml @@ -46,9 +46,12 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/1 ID: 115 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 300 K (Berger, GROMACS, 300 ns) [NMRlipids simulation 115] + name: Molecular dynamics trajectory of a POPC bilayer at 300 K (Berger, GROMACS, + 300 ns) [NMRlipids simulation 115] alternateName: 256POPC_10342SOL_300K_Berger - description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 300 K. Simulated with Berger in GROMACS for 300 ns (44338 atoms). Deposited as NMRlipids Databank simulation 115 and available from https://doi.org/10.5281/zenodo.1402417. + description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 300 K. Simulated with Berger in GROMACS for 300 ns (44338 atoms). Deposited + as NMRlipids Databank simulation 115 and available from https://doi.org/10.5281/zenodo.1402417. sameAs: https://doi.org/10.5281/zenodo.1402417 datePublished: '2018-08-23' license: diff --git a/Simulations/b2d/33a/b2d33a7c055ee947607ff0b8d90fc25eca9db160/75eca9d1bf0371e6f370b80a845bbce0e2e0c8ab/README.yaml b/Simulations/b2d/33a/b2d33a7c055ee947607ff0b8d90fc25eca9db160/75eca9d1bf0371e6f370b80a845bbce0e2e0c8ab/README.yaml index 3a26bedb6f..ece26e3334 100644 --- a/Simulations/b2d/33a/b2d33a7c055ee947607ff0b8d90fc25eca9db160/75eca9d1bf0371e6f370b80a845bbce0e2e0c8ab/README.yaml +++ b/Simulations/b2d/33a/b2d33a7c055ee947607ff0b8d90fc25eca9db160/75eca9d1bf0371e6f370b80a845bbce0e2e0c8ab/README.yaml @@ -48,9 +48,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 92 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (84:8:8) bilayer at 310 K (Lipid17, GROMACS 5.1.2, 100 ns) [NMRlipids simulation 92] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (84:8:8) bilayer at 310 K + (Lipid17, GROMACS 5.1.2, 100 ns) [NMRlipids simulation 92] alternateName: 500POPC_48SOD_48CLA_25000SOL_310K - description: Molecular dynamics trajectory of a lipid bilayer of 500 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 84 mol%), 48 CLA (8 mol%) and 48 SOD (8 mol%) at 310 K. Simulated with Lipid17 in GROMACS 5.1.2 for 100 ns (142096 atoms). Deposited as NMRlipids Databank simulation 92 and available from https://doi.org/10.5281/zenodo.2574959. + description: Molecular dynamics trajectory of a lipid bilayer of 500 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 84 mol%), 48 CLA (8 mol%) and 48 SOD (8 mol%) at 310 K. Simulated with Lipid17 + in GROMACS 5.1.2 for 100 ns (142096 atoms). Deposited as NMRlipids Databank simulation + 92 and available from https://doi.org/10.5281/zenodo.2574959. sameAs: https://doi.org/10.5281/zenodo.2574959 datePublished: '2019-02-25' license: diff --git a/Simulations/b2f/9fe/b2f9fe6308863aee7bf07bed2b237163d166b5da/cff44d14ee344a85c718f91ac4f71ec6b8cc261a/README.yaml b/Simulations/b2f/9fe/b2f9fe6308863aee7bf07bed2b237163d166b5da/cff44d14ee344a85c718f91ac4f71ec6b8cc261a/README.yaml index 8f39827b85..d8d4a14cdc 100644 --- a/Simulations/b2f/9fe/b2f9fe6308863aee7bf07bed2b237163d166b5da/cff44d14ee344a85c718f91ac4f71ec6b8cc261a/README.yaml +++ b/Simulations/b2f/9fe/b2f9fe6308863aee7bf07bed2b237163d166b5da/cff44d14ee344a85c718f91ac4f71ec6b8cc261a/README.yaml @@ -49,9 +49,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 860 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (45:36:18) bilayer at 300 K (CHARMM36, GROMACS 2019.5, 100 ns) [NMRlipids simulation 860] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (45:36:18) bilayer at 300 + K (CHARMM36, GROMACS 2019.5, 100 ns) [NMRlipids simulation 860] alternateName: POPC, 44 w/l, 300 K, 0.5 M CaCl2 - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 45 mol%), 160 CLA (36 mol%) and 80 CAL (18 mol%) at 300 K. Simulated with CHARMM36 in GROMACS 2019.5 for 100 ns (53680 atoms). Deposited as NMRlipids Databank simulation 860 and available from https://doi.org/10.5281/zenodo.6339898. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 45 mol%), 160 CLA (36 mol%) and 80 CAL (18 mol%) at 300 K. Simulated with CHARMM36 + in GROMACS 2019.5 for 100 ns (53680 atoms). Deposited as NMRlipids Databank simulation + 860 and available from https://doi.org/10.5281/zenodo.6339898. sameAs: https://doi.org/10.5281/zenodo.6339898 datePublished: '2022-03-09' license: diff --git a/Simulations/b32/5fe/b325fe9c3294adbf74b4dbee14d31a90cb0d1127/aa71f45d8b1415cfa3e21bf46752f4a3b1832633/README.yaml b/Simulations/b32/5fe/b325fe9c3294adbf74b4dbee14d31a90cb0d1127/aa71f45d8b1415cfa3e21bf46752f4a3b1832633/README.yaml index 3d848d0cef..59d2a0c3f6 100644 --- a/Simulations/b32/5fe/b325fe9c3294adbf74b4dbee14d31a90cb0d1127/aa71f45d8b1415cfa3e21bf46752f4a3b1832633/README.yaml +++ b/Simulations/b32/5fe/b325fe9c3294adbf74b4dbee14d31a90cb0d1127/aa71f45d8b1415cfa3e21bf46752f4a3b1832633/README.yaml @@ -51,9 +51,14 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 323 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPG/POT (67:17:17) bilayer at 298 K (CHARMM36, GROMACS, 200 ns) [NMRlipids simulation 323] + name: Molecular dynamics trajectory of a POPC/POPG/POT (67:17:17) bilayer at 298 + K (CHARMM36, GROMACS, 200 ns) [NMRlipids simulation 323] alternateName: 400POPC_100POPG_100POT_298K_122392Atoms - description: Molecular dynamics trajectory of a lipid bilayer of 400 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 67 mol%), 100 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 17 mol%) and 100 POT (17 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for 200 ns (122392 atoms). Deposited as NMRlipids Databank simulation 323 and available from https://doi.org/10.5281/zenodo.3483783. + description: Molecular dynamics trajectory of a lipid bilayer of 400 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 67 mol%), 100 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 17 mol%) + and 100 POT (17 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for 200 ns + (122392 atoms). Deposited as NMRlipids Databank simulation 323 and available from + https://doi.org/10.5281/zenodo.3483783. sameAs: https://doi.org/10.5281/zenodo.3483783 datePublished: '2019-10-12' license: diff --git a/Simulations/b34/f14/b34f142030a5a053e8c29eede2e333cfe5791219/ebed7ea805a058be91541f0aee4eae3ccfb4d807/README.yaml b/Simulations/b34/f14/b34f142030a5a053e8c29eede2e333cfe5791219/ebed7ea805a058be91541f0aee4eae3ccfb4d807/README.yaml index 1c2eb85d03..0fdae3a902 100644 --- a/Simulations/b34/f14/b34f142030a5a053e8c29eede2e333cfe5791219/ebed7ea805a058be91541f0aee4eae3ccfb4d807/README.yaml +++ b/Simulations/b34/f14/b34f142030a5a053e8c29eede2e333cfe5791219/ebed7ea805a058be91541f0aee4eae3ccfb4d807/README.yaml @@ -54,9 +54,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 366 bioschema_properties: - name: Molecular dynamics trajectory of a CLA/POPC/CAL (43:35:22) bilayer at 313 K (ECC-lipids, GROMACS 5.1.4, 300 ns) [NMRlipids simulation 366] + name: Molecular dynamics trajectory of a CLA/POPC/CAL (43:35:22) bilayer at 313 + K (ECC-lipids, GROMACS 5.1.4, 300 ns) [NMRlipids simulation 366] alternateName: 128POPC_6232SOL_80CAL_160CLA_313K_OPC3model - description: Molecular dynamics trajectory of a lipid bilayer of 160 CLA (43 mol%), 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 35 mol%) and 80 CAL (22 mol%) at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 300 ns (36088 atoms). Deposited as NMRlipids Databank simulation 366 and available from https://doi.org/10.5281/zenodo.1118980. + description: Molecular dynamics trajectory of a lipid bilayer of 160 CLA (43 mol%), + 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 35 mol%) and 80 CAL + (22 mol%) at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 300 ns (36088 + atoms). Deposited as NMRlipids Databank simulation 366 and available from https://doi.org/10.5281/zenodo.1118980. sameAs: https://doi.org/10.5281/zenodo.1118980 datePublished: '2017-12-19' license: @@ -146,7 +150,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1118980 identifier: 10.5281/zenodo.1118980 url: https://doi.org/10.5281/zenodo.1118980 - name: Simulations Of Popc Lipid Bilayer In Water Solution At Various Nacl And Cacl2 Concentrations Using Ecc-Popc Force Field And Various Water Models + name: Simulations Of Popc Lipid Bilayer In Water Solution At Various Nacl And + Cacl2 Concentrations Using Ecc-Popc Force Field And Various Water Models publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/b36/d0b/b36d0b412a1d5a48eb09de81083d7e7ee2e53b77/aa5fa21526aa284cf893228426300751d81d43f1/README.yaml b/Simulations/b36/d0b/b36d0b412a1d5a48eb09de81083d7e7ee2e53b77/aa5fa21526aa284cf893228426300751d81d43f1/README.yaml index b58a3f954d..2920e6a058 100644 --- a/Simulations/b36/d0b/b36d0b412a1d5a48eb09de81083d7e7ee2e53b77/aa5fa21526aa284cf893228426300751d81d43f1/README.yaml +++ b/Simulations/b36/d0b/b36d0b412a1d5a48eb09de81083d7e7ee2e53b77/aa5fa21526aa284cf893228426300751d81d43f1/README.yaml @@ -39,9 +39,13 @@ EXPERIMENT: C30: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/C30 (95:5) bilayer at 343 K (SLIPIDS, GROMACS, 100 ns) [NMRlipids simulation 896] + name: Molecular dynamics trajectory of a DPPC/C30 (95:5) bilayer at 343 K (SLIPIDS, + GROMACS, 100 ns) [NMRlipids simulation 896] alternateName: DPPC/C30 - description: Molecular dynamics trajectory of a lipid bilayer of 288 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 95 mol%) and 16 C30 (n-Triacontane, 5 mol%) at 343 K. Simulated with SLIPIDS in GROMACS for 100 ns (51875 atoms). Deposited as NMRlipids Databank simulation 896 and available from https://doi.org/10.5281/zenodo.7572990. + description: Molecular dynamics trajectory of a lipid bilayer of 288 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 95 mol%) and 16 C30 (n-Triacontane, 5 mol%) at 343 K. Simulated with SLIPIDS in + GROMACS for 100 ns (51875 atoms). Deposited as NMRlipids Databank simulation 896 + and available from https://doi.org/10.5281/zenodo.7572990. sameAs: https://doi.org/10.5281/zenodo.7572990 datePublished: '2023-01-26' license: @@ -133,7 +137,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.7572990 identifier: 10.5281/zenodo.7572990 url: https://doi.org/10.5281/zenodo.7572990 - name: 'MD simulation input files and results for ,,Atomistic MD simulations of n-alkanes in a phospholipid bilayer: CHARMM36 versus Slipids"' + name: 'MD simulation input files and results for ,,Atomistic MD simulations of + n-alkanes in a phospholipid bilayer: CHARMM36 versus Slipids"' publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/b4f/866/b4f866c0dabffa6cd891e91841591d46590f34aa/a231c358dd8c0b7bb4cf558ccdbf022373354a9a/README.yaml b/Simulations/b4f/866/b4f866c0dabffa6cd891e91841591d46590f34aa/a231c358dd8c0b7bb4cf558ccdbf022373354a9a/README.yaml index 5370214b35..1d22411be0 100644 --- a/Simulations/b4f/866/b4f866c0dabffa6cd891e91841591d46590f34aa/a231c358dd8c0b7bb4cf558ccdbf022373354a9a/README.yaml +++ b/Simulations/b4f/866/b4f866c0dabffa6cd891e91841591d46590f34aa/a231c358dd8c0b7bb4cf558ccdbf022373354a9a/README.yaml @@ -44,9 +44,12 @@ DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 428 AUTHORS_CONTACT: Buslaev Pavel bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 303 K (CHARMM36, GROMACS, 500 ns) [NMRlipids simulation 428] + name: Molecular dynamics trajectory of a POPC bilayer at 303 K (CHARMM36, GROMACS, + 500 ns) [NMRlipids simulation 428] alternateName: POPC_T303K - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 303 K. Simulated with CHARMM36 in GROMACS for 500 ns (32512 atoms). Deposited as NMRlipids Databank simulation 428 and available from https://doi.org/10.5281/zenodo.3474863. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 303 K. Simulated with CHARMM36 in GROMACS for 500 ns (32512 atoms). Deposited + as NMRlipids Databank simulation 428 and available from https://doi.org/10.5281/zenodo.3474863. sameAs: https://doi.org/10.5281/zenodo.3474863 datePublished: '2019-10-07' license: @@ -134,7 +137,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3474863 identifier: 10.5281/zenodo.3474863 url: https://doi.org/10.5281/zenodo.3474863 - name: MD simulation trajectory for POPC bilayer with 128 lipid molecules (CHARMM36, Gromacs 5.1) + name: MD simulation trajectory for POPC bilayer with 128 lipid molecules (CHARMM36, + Gromacs 5.1) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/b55/1cd/b551cd80ed2bc19ef41d62fab20717269c28acce/c628d207183a9cb471eb5f0927df800e936d2425/README.yaml b/Simulations/b55/1cd/b551cd80ed2bc19ef41d62fab20717269c28acce/c628d207183a9cb471eb5f0927df800e936d2425/README.yaml index 57257b7ef0..ff826311f1 100644 --- a/Simulations/b55/1cd/b551cd80ed2bc19ef41d62fab20717269c28acce/c628d207183a9cb471eb5f0927df800e936d2425/README.yaml +++ b/Simulations/b55/1cd/b551cd80ed2bc19ef41d62fab20717269c28acce/c628d207183a9cb471eb5f0927df800e936d2425/README.yaml @@ -59,9 +59,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 442 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/SOD/POPG/CLA (47:27:20:6) bilayer at 310 K (GROMOS-CKP, GROMACS 5.1.2, 100 ns) [NMRlipids simulation 442] + name: Molecular dynamics trajectory of a POPC/SOD/POPG/CLA (47:27:20:6) bilayer + at 310 K (GROMOS-CKP, GROMACS 5.1.2, 100 ns) [NMRlipids simulation 442] alternateName: 350POPC_150POPG_25000SOL_198SOD_48CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 350 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 47 mol%), 198 SOD (27 mol%), 150 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 20 mol%) and 48 CLA (6 mol%) at 310 K. Simulated with GROMOS-CKP in GROMACS 5.1.2 for 100 ns (101396 atoms). Deposited as NMRlipids Databank simulation 442 and available from https://doi.org/10.5281/zenodo.2582721. + description: Molecular dynamics trajectory of a lipid bilayer of 350 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 47 mol%), 198 SOD (27 mol%), 150 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, + 20 mol%) and 48 CLA (6 mol%) at 310 K. Simulated with GROMOS-CKP in GROMACS 5.1.2 + for 100 ns (101396 atoms). Deposited as NMRlipids Databank simulation 442 and + available from https://doi.org/10.5281/zenodo.2582721. sameAs: https://doi.org/10.5281/zenodo.2582721 datePublished: '2019-03-04' license: @@ -154,7 +159,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.2582721 identifier: 10.5281/zenodo.2582721 url: https://doi.org/10.5281/zenodo.2582721 - name: GROMOS-CKP POPC-POPG 7:3 Bilayer Simulation (Last 100 ns, 150 mM NaCl, 310 K ) + name: GROMOS-CKP POPC-POPG 7:3 Bilayer Simulation (Last 100 ns, 150 mM NaCl, 310 + K ) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/b55/bc5/b55bc5c5d101c5e99cbddfad5566fcebe825ebd1/93065f4158f89ad6843df172660293c2162073db/README.yaml b/Simulations/b55/bc5/b55bc5c5d101c5e99cbddfad5566fcebe825ebd1/93065f4158f89ad6843df172660293c2162073db/README.yaml index 6912a565e4..059e647358 100644 --- a/Simulations/b55/bc5/b55bc5c5d101c5e99cbddfad5566fcebe825ebd1/93065f4158f89ad6843df172660293c2162073db/README.yaml +++ b/Simulations/b55/bc5/b55bc5c5d101c5e99cbddfad5566fcebe825ebd1/93065f4158f89ad6843df172660293c2162073db/README.yaml @@ -46,9 +46,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 441 bioschema_properties: - name: Molecular dynamics trajectory of a POPG/SOD (50:50) bilayer at 310 K (Slipids, GROMACS 2018.3, 100 ns) [NMRlipids simulation 441] + name: Molecular dynamics trajectory of a POPG/SOD (50:50) bilayer at 310 K (Slipids, + GROMACS 2018.3, 100 ns) [NMRlipids simulation 441] alternateName: 500POPG_25000SOL_50SOD_310K - description: Molecular dynamics trajectory of a lipid bilayer of 500 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 50 mol%) and 500 SOD (50 mol%) at 310 K. Simulated with Slipids in GROMACS 2018.3 for 100 ns (139000 atoms). Deposited as NMRlipids Databank simulation 441 and available from https://doi.org/10.5281/zenodo.3364460. + description: Molecular dynamics trajectory of a lipid bilayer of 500 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, + 50 mol%) and 500 SOD (50 mol%) at 310 K. Simulated with Slipids in GROMACS 2018.3 + for 100 ns (139000 atoms). Deposited as NMRlipids Databank simulation 441 and + available from https://doi.org/10.5281/zenodo.3364460. sameAs: https://doi.org/10.5281/zenodo.3364460 datePublished: '2019-08-09' license: diff --git a/Simulations/b56/b24/b56b24dc9838e1bfc337c1cc2f2880a82d5f7330/09d478c46cc9c5fe4f3d50ce4ca26d28e59fd099/README.yaml b/Simulations/b56/b24/b56b24dc9838e1bfc337c1cc2f2880a82d5f7330/09d478c46cc9c5fe4f3d50ce4ca26d28e59fd099/README.yaml index fc530203d3..b4ec2e7c99 100644 --- a/Simulations/b56/b24/b56b24dc9838e1bfc337c1cc2f2880a82d5f7330/09d478c46cc9c5fe4f3d50ce4ca26d28e59fd099/README.yaml +++ b/Simulations/b56/b24/b56b24dc9838e1bfc337c1cc2f2880a82d5f7330/09d478c46cc9c5fe4f3d50ce4ca26d28e59fd099/README.yaml @@ -45,9 +45,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 207 bioschema_properties: - name: Molecular dynamics trajectory of a POPG/SOD (50:50) bilayer at 298 K (Slipids, GROMACS 5.0.4, 50 ns) [NMRlipids simulation 207] + name: Molecular dynamics trajectory of a POPG/SOD (50:50) bilayer at 298 K (Slipids, + GROMACS 5.0.4, 50 ns) [NMRlipids simulation 207] alternateName: 288POPG_10664SOL_288SOD_298K - description: Molecular dynamics trajectory of a lipid bilayer of 288 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 50 mol%) and 288 SOD (50 mol%) at 298 K. Simulated with Slipids in GROMACS 5.0.4 for 50 ns (68856 atoms). Deposited as NMRlipids Databank simulation 207 and available from https://doi.org/10.5281/zenodo.546133. + description: Molecular dynamics trajectory of a lipid bilayer of 288 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, + 50 mol%) and 288 SOD (50 mol%) at 298 K. Simulated with Slipids in GROMACS 5.0.4 + for 50 ns (68856 atoms). Deposited as NMRlipids Databank simulation 207 and available + from https://doi.org/10.5281/zenodo.546133. sameAs: https://doi.org/10.5281/zenodo.546133 datePublished: '2017-04-13' license: @@ -138,7 +142,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.546133 identifier: 10.5281/zenodo.546133 url: https://doi.org/10.5281/zenodo.546133 - name: 'Md Simulation Trajectory Of A Fully Hydrated Popg Bilayer: Slipids, Gromacs 5.0.4. 2017.' + name: 'Md Simulation Trajectory Of A Fully Hydrated Popg Bilayer: Slipids, Gromacs + 5.0.4. 2017.' publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/b58/0d1/b580d13983ed1b38cf975bc3f129c58bf05efd5a/244f4bc5e15f39de659fa2b13e30cd833084af44/README.yaml b/Simulations/b58/0d1/b580d13983ed1b38cf975bc3f129c58bf05efd5a/244f4bc5e15f39de659fa2b13e30cd833084af44/README.yaml index d28eea145a..6664010c47 100644 --- a/Simulations/b58/0d1/b580d13983ed1b38cf975bc3f129c58bf05efd5a/244f4bc5e15f39de659fa2b13e30cd833084af44/README.yaml +++ b/Simulations/b58/0d1/b580d13983ed1b38cf975bc3f129c58bf05efd5a/244f4bc5e15f39de659fa2b13e30cd833084af44/README.yaml @@ -43,9 +43,12 @@ EXPERIMENT: - 10.1021/jp511159q/1 ID: 195 bioschema_properties: - name: Molecular dynamics trajectory of a POPE bilayer at 310 K (Lipid17, GROMACS 2020.1, 100 ns) [NMRlipids simulation 195] + name: Molecular dynamics trajectory of a POPE bilayer at 310 K (Lipid17, GROMACS + 2020.1, 100 ns) [NMRlipids simulation 195] alternateName: 500POPE_25000SOL_310K - description: Molecular dynamics trajectory of a lipid bilayer of 500 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) at 310 K. Simulated with Lipid17 in GROMACS 2020.1 for 100 ns (137500 atoms). Deposited as NMRlipids Databank simulation 195 and available from https://doi.org/10.5281/zenodo.4424292. + description: Molecular dynamics trajectory of a lipid bilayer of 500 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) + at 310 K. Simulated with Lipid17 in GROMACS 2020.1 for 100 ns (137500 atoms). + Deposited as NMRlipids Databank simulation 195 and available from https://doi.org/10.5281/zenodo.4424292. sameAs: https://doi.org/10.5281/zenodo.4424292 datePublished: '2019-06-03' license: diff --git a/Simulations/b58/f0c/b58f0ce7128b1e97e4d1a90fbffe808ee2cbcc75/b58f0ce7128b1e97e4d1a90fbffe808ee2cbcc75/README.yaml b/Simulations/b58/f0c/b58f0ce7128b1e97e4d1a90fbffe808ee2cbcc75/b58f0ce7128b1e97e4d1a90fbffe808ee2cbcc75/README.yaml index 3b271b90cd..7def137fe7 100644 --- a/Simulations/b58/f0c/b58f0ce7128b1e97e4d1a90fbffe808ee2cbcc75/b58f0ce7128b1e97e4d1a90fbffe808ee2cbcc75/README.yaml +++ b/Simulations/b58/f0c/b58f0ce7128b1e97e4d1a90fbffe808ee2cbcc75/b58f0ce7128b1e97e4d1a90fbffe808ee2cbcc75/README.yaml @@ -42,9 +42,12 @@ EXPERIMENT: FORMFACTOR: - 10.1021/jp511159q/1 bioschema_properties: - name: Molecular dynamics trajectory of a POPE bilayer at 310 K (AMOEBA, OPENMM, 330 ns) [NMRlipids simulation 730] + name: Molecular dynamics trajectory of a POPE bilayer at 310 K (AMOEBA, OPENMM, + 330 ns) [NMRlipids simulation 730] alternateName: POPE_310K - description: Molecular dynamics trajectory of a lipid bilayer of 72 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) at 310 K. Simulated with AMOEBA in OPENMM for 330 ns (17640 atoms). Deposited as NMRlipids Databank simulation 730 and available from https://doi.org/10.5281/zenodo.7602924. + description: Molecular dynamics trajectory of a lipid bilayer of 72 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) + at 310 K. Simulated with AMOEBA in OPENMM for 330 ns (17640 atoms). Deposited + as NMRlipids Databank simulation 730 and available from https://doi.org/10.5281/zenodo.7602924. sameAs: https://doi.org/10.5281/zenodo.7602924 datePublished: '2023-02-03' license: diff --git a/Simulations/b5b/4d3/b5b4d3b0349e2a70da5c7b1d8b7f6284dbe3246c/b0d30b1cfe975ca6f08b67b09288dec485d3d8ad/README.yaml b/Simulations/b5b/4d3/b5b4d3b0349e2a70da5c7b1d8b7f6284dbe3246c/b0d30b1cfe975ca6f08b67b09288dec485d3d8ad/README.yaml index bd8dec4408..a65bc99f16 100644 --- a/Simulations/b5b/4d3/b5b4d3b0349e2a70da5c7b1d8b7f6284dbe3246c/b0d30b1cfe975ca6f08b67b09288dec485d3d8ad/README.yaml +++ b/Simulations/b5b/4d3/b5b4d3b0349e2a70da5c7b1d8b7f6284dbe3246c/b0d30b1cfe975ca6f08b67b09288dec485d3d8ad/README.yaml @@ -52,9 +52,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 37 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (94:4:2) bilayer at 313 K (ECC-lipids, GROMACS, 300 ns) [NMRlipids simulation 37] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (94:4:2) bilayer at 313 K + (ECC-lipids, GROMACS, 300 ns) [NMRlipids simulation 37] alternateName: 200POPC_9000SOL_4CAL_8CLA_313K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 94 mol%), 8 CLA (4 mol%) and 4 CAL (2 mol%) at 313 K. Simulated with ECC-lipids in GROMACS for 300 ns (53812 atoms). Deposited as NMRlipids Databank simulation 37 and available from https://doi.org/10.5281/zenodo.3434100. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 94 mol%), 8 CLA (4 mol%) and 4 CAL (2 mol%) at 313 K. Simulated with ECC-lipids + in GROMACS for 300 ns (53812 atoms). Deposited as NMRlipids Databank simulation + 37 and available from https://doi.org/10.5281/zenodo.3434100. sameAs: https://doi.org/10.5281/zenodo.3434100 datePublished: '2019-09-17' license: diff --git a/Simulations/b5b/c04/b5bc04ce111a8a469884eeaead2ce48c5dab9ff7/a53e18fd1c83685c8842c0cb715492e08c3e765d/README.yaml b/Simulations/b5b/c04/b5bc04ce111a8a469884eeaead2ce48c5dab9ff7/a53e18fd1c83685c8842c0cb715492e08c3e765d/README.yaml index 3fbd8de7a7..d8b9c69142 100644 --- a/Simulations/b5b/c04/b5bc04ce111a8a469884eeaead2ce48c5dab9ff7/a53e18fd1c83685c8842c0cb715492e08c3e765d/README.yaml +++ b/Simulations/b5b/c04/b5bc04ce111a8a469884eeaead2ce48c5dab9ff7/a53e18fd1c83685c8842c0cb715492e08c3e765d/README.yaml @@ -45,9 +45,12 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/1 ID: 38 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 298 K (Orange, GROMACS 4.5, 50 ns) [NMRlipids simulation 38] + name: Molecular dynamics trajectory of a POPC bilayer at 298 K (Orange, GROMACS + 4.5, 50 ns) [NMRlipids simulation 38] alternateName: 72POPC_2880SOL_298K - description: Molecular dynamics trajectory of a lipid bilayer of 72 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 298 K. Simulated with Orange in GROMACS 4.5 for 50 ns (12384 atoms). Deposited as NMRlipids Databank simulation 38 and available from https://doi.org/10.5281/zenodo.34488. + description: Molecular dynamics trajectory of a lipid bilayer of 72 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 298 K. Simulated with Orange in GROMACS 4.5 for 50 ns (12384 atoms). Deposited + as NMRlipids Databank simulation 38 and available from https://doi.org/10.5281/zenodo.34488. sameAs: https://doi.org/10.5281/zenodo.34488 datePublished: '2015-12-02' license: diff --git a/Simulations/b64/617/b64617d3ab23f535b7c272a8684b7f32717bd2bf/14c86396e0205a57609615395e9923a227bf4b9e/README.yaml b/Simulations/b64/617/b64617d3ab23f535b7c272a8684b7f32717bd2bf/14c86396e0205a57609615395e9923a227bf4b9e/README.yaml index ce8872e0e8..f2f8853ae0 100644 --- a/Simulations/b64/617/b64617d3ab23f535b7c272a8684b7f32717bd2bf/14c86396e0205a57609615395e9923a227bf4b9e/README.yaml +++ b/Simulations/b64/617/b64617d3ab23f535b7c272a8684b7f32717bd2bf/14c86396e0205a57609615395e9923a227bf4b9e/README.yaml @@ -79,9 +79,16 @@ EXPERIMENT: GM1: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPE/CHOL/SM16/POPS/GM1 (38:24:20:9:5:4) bilayer at 300 K (Charmm36, GROMACS 2020.4, 300 ns) [NMRlipids simulation 769] + name: Molecular dynamics trajectory of a POPC/POPE/CHOL/SM16/POPS/GM1 (38:24:20:9:5:4) + bilayer at 300 K (Charmm36, GROMACS 2020.4, 300 ns) [NMRlipids simulation 769] alternateName: POPC_POPE_POPS_SM_CHOL_GM1_NoIons - description: Molecular dynamics trajectory of a lipid bilayer of 152 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 38 mol%), 96 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 24 mol%), 80 CHOL (cholesterol, 20 mol%), 36 SM16 (N-palmitoyl-D-erythro-sphingosylphosphorylcholine, 9 mol%), 20 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 5 mol%) and 16 GM1 (GM1(d18:1/16:0), 4 mol%) at 300 K. Simulated with Charmm36 in GROMACS 2020.4 for 300 ns (107914 atoms). Deposited as NMRlipids Databank simulation 769 and available from https://doi.org/10.5281/zenodo.8331718. + description: Molecular dynamics trajectory of a lipid bilayer of 152 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 38 mol%), 96 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 24 mol%), + 80 CHOL (cholesterol, 20 mol%), 36 SM16 (N-palmitoyl-D-erythro-sphingosylphosphorylcholine, + 9 mol%), 20 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 5 mol%) + and 16 GM1 (GM1(d18:1/16:0), 4 mol%) at 300 K. Simulated with Charmm36 in GROMACS + 2020.4 for 300 ns (107914 atoms). Deposited as NMRlipids Databank simulation 769 + and available from https://doi.org/10.5281/zenodo.8331718. sameAs: https://doi.org/10.5281/zenodo.8331718 datePublished: '2023-09-10' license: diff --git a/Simulations/b65/203/b652030cb22578fe7b59ef3f6ea5d54f0ffc83d7/5bb25aa2cff647c0a8722169875e349574db49db/README.yaml b/Simulations/b65/203/b652030cb22578fe7b59ef3f6ea5d54f0ffc83d7/5bb25aa2cff647c0a8722169875e349574db49db/README.yaml index 0f8671243d..31e095d2ee 100644 --- a/Simulations/b65/203/b652030cb22578fe7b59ef3f6ea5d54f0ffc83d7/5bb25aa2cff647c0a8722169875e349574db49db/README.yaml +++ b/Simulations/b65/203/b652030cb22578fe7b59ef3f6ea5d54f0ffc83d7/5bb25aa2cff647c0a8722169875e349574db49db/README.yaml @@ -43,9 +43,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 807 bioschema_properties: - name: Molecular dynamics trajectory of a DMPC bilayer at 314 K (CHARMM36, GROMACS 2022.2, 480 ns) [NMRlipids simulation 807] + name: Molecular dynamics trajectory of a DMPC bilayer at 314 K (CHARMM36, GROMACS + 2022.2, 480 ns) [NMRlipids simulation 807] alternateName: 200DMPC_4kSOL_300K - description: Molecular dynamics trajectory of a lipid bilayer of 200 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) at 314 K. Simulated with CHARMM36 in GROMACS 2022.2 for 480 ns (35600 atoms). Deposited as NMRlipids Databank simulation 807 and available from https://doi.org/10.5281/zenodo.10952391. + description: Molecular dynamics trajectory of a lipid bilayer of 200 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) + at 314 K. Simulated with CHARMM36 in GROMACS 2022.2 for 480 ns (35600 atoms). + Deposited as NMRlipids Databank simulation 807 and available from https://doi.org/10.5281/zenodo.10952391. sameAs: https://doi.org/10.5281/zenodo.10952391 datePublished: '2024-04-10' license: diff --git a/Simulations/b68/566/b68566a3b3df21c923162796ed1530e2cc43427d/57c949260b6f261039d6b2839bd2e04c68fda617/README.yaml b/Simulations/b68/566/b68566a3b3df21c923162796ed1530e2cc43427d/57c949260b6f261039d6b2839bd2e04c68fda617/README.yaml index 40976915c4..c7568bd4d0 100644 --- a/Simulations/b68/566/b68566a3b3df21c923162796ed1530e2cc43427d/57c949260b6f261039d6b2839bd2e04c68fda617/README.yaml +++ b/Simulations/b68/566/b68566a3b3df21c923162796ed1530e2cc43427d/57c949260b6f261039d6b2839bd2e04c68fda617/README.yaml @@ -56,9 +56,13 @@ WARNINGS: ORIENTATION: x-normal ID: 219 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/DCHOL/CLA/SOD (73:10:9:9) bilayer at 310 K (Slipids, GROMACS, 600 ns) [NMRlipids simulation 219] + name: Molecular dynamics trajectory of a DPPC/DCHOL/CLA/SOD (73:10:9:9) bilayer + at 310 K (Slipids, GROMACS, 600 ns) [NMRlipids simulation 219] alternateName: 392DPPC_52DCHOL_17760SOL_48SOD_48CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 392 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 73 mol%), 52 DCHOL (18,19-di-nor-cholesterol, 10 mol%), 48 CLA (9 mol%) and 48 SOD (9 mol%) at 310 K. Simulated with Slipids in GROMACS for 600 ns (107872 atoms). Deposited as NMRlipids Databank simulation 219 and available from https://doi.org/10.5281/zenodo.3540513. + description: Molecular dynamics trajectory of a lipid bilayer of 392 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 73 mol%), 52 DCHOL (18,19-di-nor-cholesterol, 10 mol%), 48 CLA (9 mol%) and 48 + SOD (9 mol%) at 310 K. Simulated with Slipids in GROMACS for 600 ns (107872 atoms). + Deposited as NMRlipids Databank simulation 219 and available from https://doi.org/10.5281/zenodo.3540513. sameAs: https://doi.org/10.5281/zenodo.3540513 datePublished: '2019-11-13' license: diff --git a/Simulations/b6f/7a3/b6f7a30913194369e3c1bb7909dab58755a84048/aac2e714b1f8afb02aa4e8cfcef7d5ce2e2adeee/README.yaml b/Simulations/b6f/7a3/b6f7a30913194369e3c1bb7909dab58755a84048/aac2e714b1f8afb02aa4e8cfcef7d5ce2e2adeee/README.yaml index b9bfd27c7b..2d0832e703 100644 --- a/Simulations/b6f/7a3/b6f7a30913194369e3c1bb7909dab58755a84048/aac2e714b1f8afb02aa4e8cfcef7d5ce2e2adeee/README.yaml +++ b/Simulations/b6f/7a3/b6f7a30913194369e3c1bb7909dab58755a84048/aac2e714b1f8afb02aa4e8cfcef7d5ce2e2adeee/README.yaml @@ -43,9 +43,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 73 bioschema_properties: - name: Molecular dynamics trajectory of a POPS/POT (50:50) bilayer at 298 K (CHARMM36, GROMACS, 100 ns) [NMRlipids simulation 73] + name: Molecular dynamics trajectory of a POPS/POT (50:50) bilayer at 298 K (CHARMM36, + GROMACS, 100 ns) [NMRlipids simulation 73] alternateName: 128POPS_128POT_4480SOL_298K_v1 - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 50 mol%) and 128 POT (50 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for 100 ns (29824 atoms). Deposited as NMRlipids Databank simulation 73 and available from https://doi.org/10.5281/zenodo.1182654. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, + 50 mol%) and 128 POT (50 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for + 100 ns (29824 atoms). Deposited as NMRlipids Databank simulation 73 and available + from https://doi.org/10.5281/zenodo.1182654. sameAs: https://doi.org/10.5281/zenodo.1182654 datePublished: '2018-02-21' license: @@ -131,7 +135,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1182654 identifier: 10.5281/zenodo.1182654 url: https://doi.org/10.5281/zenodo.1182654 - name: Charmm36 Pops Simulations (Versions 1 And 2) 298 K 1.0 Nm Lj Switching With K Ions + name: Charmm36 Pops Simulations (Versions 1 And 2) 298 K 1.0 Nm Lj Switching With + K Ions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/b76/8e9/b768e968503ac098a6e14299917f7fea8f738f91/276850e8eaf5ac3300a18244fd46e70a2d4e4c91/README.yaml b/Simulations/b76/8e9/b768e968503ac098a6e14299917f7fea8f738f91/276850e8eaf5ac3300a18244fd46e70a2d4e4c91/README.yaml index 0060fbc054..7d02d0275a 100644 --- a/Simulations/b76/8e9/b768e968503ac098a6e14299917f7fea8f738f91/276850e8eaf5ac3300a18244fd46e70a2d4e4c91/README.yaml +++ b/Simulations/b76/8e9/b768e968503ac098a6e14299917f7fea8f738f91/276850e8eaf5ac3300a18244fd46e70a2d4e4c91/README.yaml @@ -44,9 +44,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 614 bioschema_properties: - name: Molecular dynamics trajectory of a DLPC bilayer at 300 K (Berger-DLPC-13, GROMACS 4.5.4, 80 ns) [NMRlipids simulation 614] + name: Molecular dynamics trajectory of a DLPC bilayer at 300 K (Berger-DLPC-13, + GROMACS 4.5.4, 80 ns) [NMRlipids simulation 614] alternateName: 72DLPC_1152SOL_300K - description: Molecular dynamics trajectory of a lipid bilayer of 72 DLPC (1,2-dilauroyl-sn-glycero-3-phosphocholine) at 300 K. Simulated with Berger-DLPC-13 in GROMACS 4.5.4 for 80 ns (6480 atoms). Deposited as NMRlipids Databank simulation 614 and available from https://doi.org/10.5281/zenodo.16292. + description: Molecular dynamics trajectory of a lipid bilayer of 72 DLPC (1,2-dilauroyl-sn-glycero-3-phosphocholine) + at 300 K. Simulated with Berger-DLPC-13 in GROMACS 4.5.4 for 80 ns (6480 atoms). + Deposited as NMRlipids Databank simulation 614 and available from https://doi.org/10.5281/zenodo.16292. sameAs: https://doi.org/10.5281/zenodo.16292 datePublished: '2015-03-24' license: diff --git a/Simulations/b7a/4c6/b7a4c62a0f6112eb07c99e3fe912bd5e55e1dca2/5e824ebda9f3c3341685c5aa5a3ff3ad7ead34f5/README.yaml b/Simulations/b7a/4c6/b7a4c62a0f6112eb07c99e3fe912bd5e55e1dca2/5e824ebda9f3c3341685c5aa5a3ff3ad7ead34f5/README.yaml index 738ca4b245..9889b64952 100644 --- a/Simulations/b7a/4c6/b7a4c62a0f6112eb07c99e3fe912bd5e55e1dca2/5e824ebda9f3c3341685c5aa5a3ff3ad7ead34f5/README.yaml +++ b/Simulations/b7a/4c6/b7a4c62a0f6112eb07c99e3fe912bd5e55e1dca2/5e824ebda9f3c3341685c5aa5a3ff3ad7ead34f5/README.yaml @@ -43,9 +43,12 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 67 bioschema_properties: - name: Molecular dynamics trajectory of a POPE bilayer at 310 K (CHARMM36, GROMACS 2018.3, 100 ns) [NMRlipids simulation 67] + name: Molecular dynamics trajectory of a POPE bilayer at 310 K (CHARMM36, GROMACS + 2018.3, 100 ns) [NMRlipids simulation 67] alternateName: 500POPE_25000SOL_310K - description: Molecular dynamics trajectory of a lipid bilayer of 500 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) at 310 K. Simulated with CHARMM36 in GROMACS 2018.3 for 100 ns (137500 atoms). Deposited as NMRlipids Databank simulation 67 and available from https://doi.org/10.5281/zenodo.3237461. + description: Molecular dynamics trajectory of a lipid bilayer of 500 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) + at 310 K. Simulated with CHARMM36 in GROMACS 2018.3 for 100 ns (137500 atoms). + Deposited as NMRlipids Databank simulation 67 and available from https://doi.org/10.5281/zenodo.3237461. sameAs: https://doi.org/10.5281/zenodo.3237461 datePublished: '2019-06-03' license: diff --git a/Simulations/b86/c00/b86c00db1e4696dc7fa04770509c1cea31d4bf63/3c4f254f6ac8cba7eb9b53b430acba33ec2f5ce7/README.yaml b/Simulations/b86/c00/b86c00db1e4696dc7fa04770509c1cea31d4bf63/3c4f254f6ac8cba7eb9b53b430acba33ec2f5ce7/README.yaml index e87f76c118..5991624910 100644 --- a/Simulations/b86/c00/b86c00db1e4696dc7fa04770509c1cea31d4bf63/3c4f254f6ac8cba7eb9b53b430acba33ec2f5ce7/README.yaml +++ b/Simulations/b86/c00/b86c00db1e4696dc7fa04770509c1cea31d4bf63/3c4f254f6ac8cba7eb9b53b430acba33ec2f5ce7/README.yaml @@ -54,9 +54,13 @@ TRJLENGTH: 200010.0 DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 238 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/DHMDMAB (36:32:32) bilayer at 313 K (CHARMM36, GROMACS, 200 ns) [NMRlipids simulation 238] + name: Molecular dynamics trajectory of a POPC/CLA/DHMDMAB (36:32:32) bilayer at + 313 K (CHARMM36, GROMACS, 200 ns) [NMRlipids simulation 238] alternateName: POPC50%DHMDMAB_T313K - description: Molecular dynamics trajectory of a lipid bilayer of 100 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 36 mol%), 88 CLA (32 mol%) and 88 DHMDMAB (dihexadecyldimethylammonium, 32 mol%) at 313 K. Simulated with CHARMM36 in GROMACS for 200 ns (46802 atoms). Deposited as NMRlipids Databank simulation 238 and available from https://doi.org/10.5281/zenodo.1288297. + description: Molecular dynamics trajectory of a lipid bilayer of 100 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 36 mol%), 88 CLA (32 mol%) and 88 DHMDMAB (dihexadecyldimethylammonium, 32 mol%) + at 313 K. Simulated with CHARMM36 in GROMACS for 200 ns (46802 atoms). Deposited + as NMRlipids Databank simulation 238 and available from https://doi.org/10.5281/zenodo.1288297. sameAs: https://doi.org/10.5281/zenodo.1288297 datePublished: '2018-06-13' license: diff --git a/Simulations/b86/e1d/b86e1d05121438d07f56d447bf4a0ec1add4af0c/b7cad43d5423af6dee7da746eabe48b79e79c271/README.yaml b/Simulations/b86/e1d/b86e1d05121438d07f56d447bf4a0ec1add4af0c/b7cad43d5423af6dee7da746eabe48b79e79c271/README.yaml index 161a4b0bcc..da2f54866e 100644 --- a/Simulations/b86/e1d/b86e1d05121438d07f56d447bf4a0ec1add4af0c/b7cad43d5423af6dee7da746eabe48b79e79c271/README.yaml +++ b/Simulations/b86/e1d/b86e1d05121438d07f56d447bf4a0ec1add4af0c/b7cad43d5423af6dee7da746eabe48b79e79c271/README.yaml @@ -62,9 +62,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 237 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL/POPS/SOD (37:32:16:7:7) bilayer at 298 K (ECC-lipids, SPC/E water model, ECC-ions, GROMACS 2018.0, 1541 ns) [NMRlipids simulation 237] + name: Molecular dynamics trajectory of a POPC/CLA/CAL/POPS/SOD (37:32:16:7:7) bilayer + at 298 K (ECC-lipids, SPC/E water model, ECC-ions, GROMACS 2018.0, 1541 ns) [NMRlipids + simulation 237] alternateName: 12POPS_60POPC_3522SOL_26CAL_52CLA_12SOD_298K - description: Molecular dynamics trajectory of a lipid bilayer of 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 37 mol%), 52 CLA (32 mol%), 26 CAL (16 mol%), 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 7 mol%) and 12 SOD (7 mol%) at 298 K. Simulated with ECC-lipids, SPC/E water model, ECC-ions in GROMACS 2018.0 for 1541 ns (20220 atoms). Deposited as NMRlipids Databank simulation 237 and available from https://doi.org/10.5281/zenodo.1488102. + description: Molecular dynamics trajectory of a lipid bilayer of 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 37 mol%), 52 CLA (32 mol%), 26 CAL (16 mol%), 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, + 7 mol%) and 12 SOD (7 mol%) at 298 K. Simulated with ECC-lipids, SPC/E water model, + ECC-ions in GROMACS 2018.0 for 1541 ns (20220 atoms). Deposited as NMRlipids Databank + simulation 237 and available from https://doi.org/10.5281/zenodo.1488102. sameAs: https://doi.org/10.5281/zenodo.1488102 datePublished: '2018-11-14' license: @@ -157,7 +163,9 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1488102 identifier: 10.5281/zenodo.1488102 url: https://doi.org/10.5281/zenodo.1488102 - name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS (5:1) with ECC-lipids force field, and Na+ (K+) counterions at various CaCl2 additional concentrations + name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS + (5:1) with ECC-lipids force field, and Na+ (K+) counterions at various CaCl2 + additional concentrations publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/b94/5bf/b945bfffcbc41fd336254c64ea3d469a8244c9cf/8c163cc80fa8fd38e5f090ffb2626b10594470d0/README.yaml b/Simulations/b94/5bf/b945bfffcbc41fd336254c64ea3d469a8244c9cf/8c163cc80fa8fd38e5f090ffb2626b10594470d0/README.yaml index 27c9e85cc1..029efefba7 100644 --- a/Simulations/b94/5bf/b945bfffcbc41fd336254c64ea3d469a8244c9cf/8c163cc80fa8fd38e5f090ffb2626b10594470d0/README.yaml +++ b/Simulations/b94/5bf/b945bfffcbc41fd336254c64ea3d469a8244c9cf/8c163cc80fa8fd38e5f090ffb2626b10594470d0/README.yaml @@ -49,9 +49,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 561 bioschema_properties: - name: Molecular dynamics trajectory of a POPE/CLA/SOD (83:8:8) bilayer at 310 K (Slipids, GROMACS 5.1.2, 100 ns) [NMRlipids simulation 561] + name: Molecular dynamics trajectory of a POPE/CLA/SOD (83:8:8) bilayer at 310 K + (Slipids, GROMACS 5.1.2, 100 ns) [NMRlipids simulation 561] alternateName: 500POPE_25000SOL_50SOD_50CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 500 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 83 mol%), 50 CLA (8 mol%) and 50 SOD (8 mol%) at 310 K. Simulated with Slipids in GROMACS 5.1.2 for 100 ns (137600 atoms). Deposited as NMRlipids Databank simulation 561 and available from https://doi.org/10.5281/zenodo.2578069. + description: Molecular dynamics trajectory of a lipid bilayer of 500 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, + 83 mol%), 50 CLA (8 mol%) and 50 SOD (8 mol%) at 310 K. Simulated with Slipids + in GROMACS 5.1.2 for 100 ns (137600 atoms). Deposited as NMRlipids Databank simulation + 561 and available from https://doi.org/10.5281/zenodo.2578069. sameAs: https://doi.org/10.5281/zenodo.2578069 datePublished: '2019-02-25' license: diff --git a/Simulations/b97/be6/b97be660f8dbcc6b78c46a6494eb79efffdbffd7/0d4ae597205b534d766edb805ebf3047218b3432/README.yaml b/Simulations/b97/be6/b97be660f8dbcc6b78c46a6494eb79efffdbffd7/0d4ae597205b534d766edb805ebf3047218b3432/README.yaml index d0a80cc37e..0ca6974673 100644 --- a/Simulations/b97/be6/b97be660f8dbcc6b78c46a6494eb79efffdbffd7/0d4ae597205b534d766edb805ebf3047218b3432/README.yaml +++ b/Simulations/b97/be6/b97be660f8dbcc6b78c46a6494eb79efffdbffd7/0d4ae597205b534d766edb805ebf3047218b3432/README.yaml @@ -49,9 +49,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/5 ID: 662 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (80:20) bilayer at 298.15 K (Lipid17, GROMACS 2021, 1001 ns) [NMRlipids simulation 662] + name: Molecular dynamics trajectory of a POPC/CHOL (80:20) bilayer at 298.15 K (Lipid17, + GROMACS 2021, 1001 ns) [NMRlipids simulation 662] alternateName: Lipid17_POPC_CHOL20_S - description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 80 mol%) and 16 CHOL (cholesterol, 20 mol%) at 298.15 K. Simulated with Lipid17 in GROMACS 2021 for 1001 ns (21760 atoms). Deposited as NMRlipids Databank simulation 662 and available from https://doi.org/10.5281/zenodo.6992065. + description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 80 mol%) and 16 CHOL (cholesterol, 20 mol%) at 298.15 K. Simulated with Lipid17 + in GROMACS 2021 for 1001 ns (21760 atoms). Deposited as NMRlipids Databank simulation + 662 and available from https://doi.org/10.5281/zenodo.6992065. sameAs: https://doi.org/10.5281/zenodo.6992065 datePublished: '2022-08-15' license: diff --git a/Simulations/b9c/76a/b9c76a7f140b3ed219b91502a3f71aa811140a0d/2e13643638392fb362fda3742152f679a2cb453e/README.yaml b/Simulations/b9c/76a/b9c76a7f140b3ed219b91502a3f71aa811140a0d/2e13643638392fb362fda3742152f679a2cb453e/README.yaml index 106624a5b5..5c44088d79 100644 --- a/Simulations/b9c/76a/b9c76a7f140b3ed219b91502a3f71aa811140a0d/2e13643638392fb362fda3742152f679a2cb453e/README.yaml +++ b/Simulations/b9c/76a/b9c76a7f140b3ed219b91502a3f71aa811140a0d/2e13643638392fb362fda3742152f679a2cb453e/README.yaml @@ -45,9 +45,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 128 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 298 K (Berger delivered by Peter Tieleman, GROMACS 4.5, 60 ns) [NMRlipids simulation 128] + name: Molecular dynamics trajectory of a POPC bilayer at 298 K (Berger delivered + by Peter Tieleman, GROMACS 4.5, 60 ns) [NMRlipids simulation 128] alternateName: 128POPC_896SOL_298K_Berger - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 298 K. Simulated with Berger delivered by Peter Tieleman in GROMACS 4.5 for 60 ns (9344 atoms). Deposited as NMRlipids Databank simulation 128 and available from https://doi.org/10.5281/zenodo.13814. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 298 K. Simulated with Berger delivered by Peter Tieleman in GROMACS 4.5 for + 60 ns (9344 atoms). Deposited as NMRlipids Databank simulation 128 and available + from https://doi.org/10.5281/zenodo.13814. sameAs: https://doi.org/10.5281/zenodo.13814 datePublished: '2015-01-08' license: @@ -135,7 +139,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.13814 identifier: 10.5281/zenodo.13814 url: https://doi.org/10.5281/zenodo.13814 - name: Md Simulation Trajectory And Related Files For Popc Bilayer In Low Hydration (Berger Model Delivered By Tieleman, Gromacs 4.5) + name: Md Simulation Trajectory And Related Files For Popc Bilayer In Low Hydration + (Berger Model Delivered By Tieleman, Gromacs 4.5) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/ba2/d98/ba2d9804e770c2c4d40c9f45981adbea446d17d5/ac4d43f168d107273573bbc106c35eb26b25a9c7/README.yaml b/Simulations/ba2/d98/ba2d9804e770c2c4d40c9f45981adbea446d17d5/ac4d43f168d107273573bbc106c35eb26b25a9c7/README.yaml index d7fe57ec46..f023952e5a 100644 --- a/Simulations/ba2/d98/ba2d9804e770c2c4d40c9f45981adbea446d17d5/ac4d43f168d107273573bbc106c35eb26b25a9c7/README.yaml +++ b/Simulations/ba2/d98/ba2d9804e770c2c4d40c9f45981adbea446d17d5/ac4d43f168d107273573bbc106c35eb26b25a9c7/README.yaml @@ -49,9 +49,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 454 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (48:35:17) bilayer at 330 K (Slipids with ECC-scaled ions (Kohagen), GROMACS 4.6, 800 ns) [NMRlipids simulation 454] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (48:35:17) bilayer at 330 + K (Slipids with ECC-scaled ions (Kohagen), GROMACS 4.6, 800 ns) [NMRlipids simulation + 454] alternateName: 200POPC_9000SOL_73CAL_146CLA_330K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 48 mol%), 146 CLA (35 mol%) and 73 CAL (17 mol%) at 330 K. Simulated with Slipids with ECC-scaled ions (Kohagen) in GROMACS 4.6 for 800 ns (54019 atoms). Deposited as NMRlipids Databank simulation 454 and available from https://doi.org/10.5281/zenodo.259354. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 48 mol%), 146 CLA (35 mol%) and 73 CAL (17 mol%) at 330 K. Simulated with Slipids + with ECC-scaled ions (Kohagen) in GROMACS 4.6 for 800 ns (54019 atoms). Deposited + as NMRlipids Databank simulation 454 and available from https://doi.org/10.5281/zenodo.259354. sameAs: https://doi.org/10.5281/zenodo.259354 datePublished: '2017-01-24' license: @@ -139,7 +144,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.259354 identifier: 10.5281/zenodo.259354 url: https://doi.org/10.5281/zenodo.259354 - name: Popc With Varying Amounts Of Cholesterol, 450 Mm Of Cacl_2. Slipids With Ecc-Scaled Ions + name: Popc With Varying Amounts Of Cholesterol, 450 Mm Of Cacl_2. Slipids With + Ecc-Scaled Ions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/ba3/727/ba372741f420cda9bebff9601d2a3ddf91a88a04/d05108e0e40c1e51219fcd0ace52288b2f3413bc/README.yaml b/Simulations/ba3/727/ba372741f420cda9bebff9601d2a3ddf91a88a04/d05108e0e40c1e51219fcd0ace52288b2f3413bc/README.yaml index 7b7494633b..fac4388d15 100644 --- a/Simulations/ba3/727/ba372741f420cda9bebff9601d2a3ddf91a88a04/d05108e0e40c1e51219fcd0ace52288b2f3413bc/README.yaml +++ b/Simulations/ba3/727/ba372741f420cda9bebff9601d2a3ddf91a88a04/d05108e0e40c1e51219fcd0ace52288b2f3413bc/README.yaml @@ -37,9 +37,12 @@ EXPERIMENT: POPE: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a POPE bilayer at 300 K (OpenFF, GROMACS, 200 ns) [NMRlipids simulation 791] + name: Molecular dynamics trajectory of a POPE bilayer at 300 K (OpenFF, GROMACS, + 200 ns) [NMRlipids simulation 791] alternateName: POPE_128_OPENFF_300K - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) at 300 K. Simulated with OpenFF in GROMACS for 200 ns (31000 atoms). Deposited as NMRlipids Databank simulation 791 and available from https://doi.org/10.5281/zenodo.8411733. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) + at 300 K. Simulated with OpenFF in GROMACS for 200 ns (31000 atoms). Deposited + as NMRlipids Databank simulation 791 and available from https://doi.org/10.5281/zenodo.8411733. sameAs: https://doi.org/10.5281/zenodo.8411733 datePublished: '2023-10-06' license: diff --git a/Simulations/ba4/f1e/ba4f1e6a45507797acdef4358517703b0476a4ca/a71d995219262c1bfa77b5095fcc8882404d641b/README.yaml b/Simulations/ba4/f1e/ba4f1e6a45507797acdef4358517703b0476a4ca/a71d995219262c1bfa77b5095fcc8882404d641b/README.yaml index c9838ad01c..cb87c83d30 100644 --- a/Simulations/ba4/f1e/ba4f1e6a45507797acdef4358517703b0476a4ca/a71d995219262c1bfa77b5095fcc8882404d641b/README.yaml +++ b/Simulations/ba4/f1e/ba4f1e6a45507797acdef4358517703b0476a4ca/a71d995219262c1bfa77b5095fcc8882404d641b/README.yaml @@ -54,9 +54,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 191 bioschema_properties: - name: Molecular dynamics trajectory of a CLA/POPC/CAL (43:35:22) bilayer at 313 K (ECC-lipids, GROMACS 5.1.4, 300 ns) [NMRlipids simulation 191] + name: Molecular dynamics trajectory of a CLA/POPC/CAL (43:35:22) bilayer at 313 + K (ECC-lipids, GROMACS 5.1.4, 300 ns) [NMRlipids simulation 191] alternateName: 128POPC_6232SOL_80CAL_160CLA_313K_OPC4model - description: Molecular dynamics trajectory of a lipid bilayer of 160 CLA (43 mol%), 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 35 mol%) and 80 CAL (22 mol%) at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 300 ns (42320 atoms). Deposited as NMRlipids Databank simulation 191 and available from https://doi.org/10.5281/zenodo.1118980. + description: Molecular dynamics trajectory of a lipid bilayer of 160 CLA (43 mol%), + 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 35 mol%) and 80 CAL + (22 mol%) at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 300 ns (42320 + atoms). Deposited as NMRlipids Databank simulation 191 and available from https://doi.org/10.5281/zenodo.1118980. sameAs: https://doi.org/10.5281/zenodo.1118980 datePublished: '2017-12-19' license: @@ -146,7 +150,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1118980 identifier: 10.5281/zenodo.1118980 url: https://doi.org/10.5281/zenodo.1118980 - name: Simulations Of Popc Lipid Bilayer In Water Solution At Various Nacl And Cacl2 Concentrations Using Ecc-Popc Force Field And Various Water Models + name: Simulations Of Popc Lipid Bilayer In Water Solution At Various Nacl And + Cacl2 Concentrations Using Ecc-Popc Force Field And Various Water Models publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/ba8/888/ba888896d74d078c25b29ae4c106c0096146205f/7ac0f9ece8f6b64afaefad36e542a4162bac4b33/README.yaml b/Simulations/ba8/888/ba888896d74d078c25b29ae4c106c0096146205f/7ac0f9ece8f6b64afaefad36e542a4162bac4b33/README.yaml index 1f81432511..0bd71da9d4 100644 --- a/Simulations/ba8/888/ba888896d74d078c25b29ae4c106c0096146205f/7ac0f9ece8f6b64afaefad36e542a4162bac4b33/README.yaml +++ b/Simulations/ba8/888/ba888896d74d078c25b29ae4c106c0096146205f/7ac0f9ece8f6b64afaefad36e542a4162bac4b33/README.yaml @@ -44,9 +44,12 @@ WARNINGS: PBC: hexagonal-box ID: 74 bioschema_properties: - name: Molecular dynamics trajectory of a POPE bilayer at 310 K (Slipids, GROMACS 5.0.6, 100 ns) [NMRlipids simulation 74] + name: Molecular dynamics trajectory of a POPE bilayer at 310 K (Slipids, GROMACS + 5.0.6, 100 ns) [NMRlipids simulation 74] alternateName: 336POPE_13460SOL_310K_v2 - description: Molecular dynamics trajectory of a lipid bilayer of 336 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) at 310 K. Simulated with Slipids in GROMACS 5.0.6 for 100 ns (82380 atoms). Deposited as NMRlipids Databank simulation 74 and available from https://doi.org/10.5281/zenodo.1293813. + description: Molecular dynamics trajectory of a lipid bilayer of 336 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) + at 310 K. Simulated with Slipids in GROMACS 5.0.6 for 100 ns (82380 atoms). Deposited + as NMRlipids Databank simulation 74 and available from https://doi.org/10.5281/zenodo.1293813. sameAs: https://doi.org/10.5281/zenodo.1293813 datePublished: '2018-06-20' license: diff --git a/Simulations/bbe/9f2/bbe9f2ea0f3ffef918a8c0686a03bb34d85c244c/76f556a28bef20b108f17c84f5dfd576c79a3efa/README.yaml b/Simulations/bbe/9f2/bbe9f2ea0f3ffef918a8c0686a03bb34d85c244c/76f556a28bef20b108f17c84f5dfd576c79a3efa/README.yaml index 37dec8a792..47dad0042a 100644 --- a/Simulations/bbe/9f2/bbe9f2ea0f3ffef918a8c0686a03bb34d85c244c/76f556a28bef20b108f17c84f5dfd576c79a3efa/README.yaml +++ b/Simulations/bbe/9f2/bbe9f2ea0f3ffef918a8c0686a03bb34d85c244c/76f556a28bef20b108f17c84f5dfd576c79a3efa/README.yaml @@ -54,9 +54,14 @@ EXPERIMENT: POPE: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a NH4/POPI/POPE (44:44:11) bilayer at 310 K (CHARMM36, GROMACS 2022.4, 500 ns) [NMRlipids simulation 854] + name: Molecular dynamics trajectory of a NH4/POPI/POPE (44:44:11) bilayer at 310 + K (CHARMM36, GROMACS 2022.4, 500 ns) [NMRlipids simulation 854] alternateName: POPI-POPE (80:20), full hydration, 310 K, NH4+ counter ions - description: Molecular dynamics trajectory of a lipid bilayer of 160 NH4 (44 mol%), 160 POPI (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoinositol, 44 mol%) and 40 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 11 mol%) at 310 K. Simulated with CHARMM36 in GROMACS 2022.4 for 500 ns (57720 atoms). Deposited as NMRlipids Databank simulation 854 and available from https://doi.org/10.5281/zenodo.10259847. + description: Molecular dynamics trajectory of a lipid bilayer of 160 NH4 (44 mol%), + 160 POPI (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoinositol, 44 mol%) and 40 POPE + (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 11 mol%) at 310 K. Simulated + with CHARMM36 in GROMACS 2022.4 for 500 ns (57720 atoms). Deposited as NMRlipids + Databank simulation 854 and available from https://doi.org/10.5281/zenodo.10259847. sameAs: https://doi.org/10.5281/zenodo.10259847 datePublished: '2023-12-18' license: diff --git a/Simulations/bc2/420/bc242096f452160a6e7f744e3892142c984dabd9/a66cb1920a2e35920730dcf1418628186140b583/README.yaml b/Simulations/bc2/420/bc242096f452160a6e7f744e3892142c984dabd9/a66cb1920a2e35920730dcf1418628186140b583/README.yaml index b03bec528f..f222af948c 100644 --- a/Simulations/bc2/420/bc242096f452160a6e7f744e3892142c984dabd9/a66cb1920a2e35920730dcf1418628186140b583/README.yaml +++ b/Simulations/bc2/420/bc242096f452160a6e7f744e3892142c984dabd9/a66cb1920a2e35920730dcf1418628186140b583/README.yaml @@ -44,9 +44,12 @@ EXPERIMENT: - 10.1016/j.bbamem.2011.07.022/20 ID: 42 bioschema_properties: - name: Molecular dynamics trajectory of a DMPC bilayer at 333.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 42] + name: Molecular dynamics trajectory of a DMPC bilayer at 333.15 K (CHARMM36, GROMACS, + 1001 ns) [NMRlipids simulation 42] alternateName: 256DMPC_12800SOL_333K - description: Molecular dynamics trajectory of a lipid bilayer of 256 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (68608 atoms). Deposited as NMRlipids Databank simulation 42 and available from https://doi.org/10.5281/zenodo.6943413. + description: Molecular dynamics trajectory of a lipid bilayer of 256 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) + at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (68608 atoms). Deposited + as NMRlipids Databank simulation 42 and available from https://doi.org/10.5281/zenodo.6943413. sameAs: https://doi.org/10.5281/zenodo.6943413 datePublished: '2022-07-30' license: @@ -136,7 +139,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.6943413 identifier: 10.5281/zenodo.6943413 url: https://doi.org/10.5281/zenodo.6943413 - name: Simulations of different single-component bilayers, three different system sizes + name: Simulations of different single-component bilayers, three different system + sizes publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/bca/83f/bca83f586f696c784a2c7b413395737990948bb0/e56d0b29eab3f38a6cae0c26c63368974b628922/README.yaml b/Simulations/bca/83f/bca83f586f696c784a2c7b413395737990948bb0/e56d0b29eab3f38a6cae0c26c63368974b628922/README.yaml index 2cb545cf10..87e3e50ed1 100644 --- a/Simulations/bca/83f/bca83f586f696c784a2c7b413395737990948bb0/e56d0b29eab3f38a6cae0c26c63368974b628922/README.yaml +++ b/Simulations/bca/83f/bca83f586f696c784a2c7b413395737990948bb0/e56d0b29eab3f38a6cae0c26c63368974b628922/README.yaml @@ -49,9 +49,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 60 bioschema_properties: - name: Molecular dynamics trajectory of a DAPC/CHOL (90:10) bilayer at 310 K (CHARMM36, GROMACS, 2000 ns) [NMRlipids simulation 60] + name: Molecular dynamics trajectory of a DAPC/CHOL (90:10) bilayer at 310 K (CHARMM36, + GROMACS, 2000 ns) [NMRlipids simulation 60] alternateName: 260DAPC_28CHOL_11520SOL_310K - description: Molecular dynamics trajectory of a lipid bilayer of 260 DAPC (1,2-diarachidonoyl-sn-glycero-3-phosphocholine, 90 mol%) and 28 CHOL (cholesterol, 10 mol%) at 310 K. Simulated with CHARMM36 in GROMACS for 2000 ns (72512 atoms). Deposited as NMRlipids Databank simulation 60 and available from https://doi.org/10.5281/zenodo.2653735. + description: Molecular dynamics trajectory of a lipid bilayer of 260 DAPC (1,2-diarachidonoyl-sn-glycero-3-phosphocholine, + 90 mol%) and 28 CHOL (cholesterol, 10 mol%) at 310 K. Simulated with CHARMM36 + in GROMACS for 2000 ns (72512 atoms). Deposited as NMRlipids Databank simulation + 60 and available from https://doi.org/10.5281/zenodo.2653735. sameAs: https://doi.org/10.5281/zenodo.2653735 datePublished: '2019-04-29' license: @@ -140,7 +144,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.2653735 identifier: 10.5281/zenodo.2653735 url: https://doi.org/10.5281/zenodo.2653735 - name: Atomistic simulations of DAPC/cholesterol bilayers with one cholesterol restrained to the membrane core + name: Atomistic simulations of DAPC/cholesterol bilayers with one cholesterol + restrained to the membrane core publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/bcf/4b1/bcf4b194b7312e8a2e8001a271bc4e6f1a7ec02d/23bf9b7088bceeb0d6a99884d4bc9acfd8dd60c4/README.yaml b/Simulations/bcf/4b1/bcf4b194b7312e8a2e8001a271bc4e6f1a7ec02d/23bf9b7088bceeb0d6a99884d4bc9acfd8dd60c4/README.yaml index ebf45c47b5..b204b75922 100644 --- a/Simulations/bcf/4b1/bcf4b194b7312e8a2e8001a271bc4e6f1a7ec02d/23bf9b7088bceeb0d6a99884d4bc9acfd8dd60c4/README.yaml +++ b/Simulations/bcf/4b1/bcf4b194b7312e8a2e8001a271bc4e6f1a7ec02d/23bf9b7088bceeb0d6a99884d4bc9acfd8dd60c4/README.yaml @@ -40,9 +40,12 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 123 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 303 K (CHARMM36, GROMACS 5.0.6, 500 ns) [NMRlipids simulation 123] + name: Molecular dynamics trajectory of a POPC bilayer at 303 K (CHARMM36, GROMACS + 5.0.6, 500 ns) [NMRlipids simulation 123] alternateName: 128POPC_5120SOL_10A-switch_v4 - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 303 K. Simulated with CHARMM36 in GROMACS 5.0.6 for 500 ns (32512 atoms). Deposited as NMRlipids Databank simulation 123 and available from https://doi.org/10.5281/zenodo.164206. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 303 K. Simulated with CHARMM36 in GROMACS 5.0.6 for 500 ns (32512 atoms). Deposited + as NMRlipids Databank simulation 123 and available from https://doi.org/10.5281/zenodo.164206. sameAs: https://doi.org/10.5281/zenodo.164206 datePublished: '2016-11-01' license: diff --git a/Simulations/bd9/801/bd98012f8548b7c22429790489240ca0e79aeb83/0fd7285aeef1d21f45deec3262aa06cd18f50df5/README.yaml b/Simulations/bd9/801/bd98012f8548b7c22429790489240ca0e79aeb83/0fd7285aeef1d21f45deec3262aa06cd18f50df5/README.yaml index ea3b9ff1ec..38eaea3f41 100644 --- a/Simulations/bd9/801/bd98012f8548b7c22429790489240ca0e79aeb83/0fd7285aeef1d21f45deec3262aa06cd18f50df5/README.yaml +++ b/Simulations/bd9/801/bd98012f8548b7c22429790489240ca0e79aeb83/0fd7285aeef1d21f45deec3262aa06cd18f50df5/README.yaml @@ -40,9 +40,12 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 99 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 303 K (CHARMM36, GROMACS 5.0.6, 500 ns) [NMRlipids simulation 99] + name: Molecular dynamics trajectory of a POPC bilayer at 303 K (CHARMM36, GROMACS + 5.0.6, 500 ns) [NMRlipids simulation 99] alternateName: 128POPC_5120SOL_10A-switch_v2 - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 303 K. Simulated with CHARMM36 in GROMACS 5.0.6 for 500 ns (32512 atoms). Deposited as NMRlipids Databank simulation 99 and available from https://doi.org/10.5281/zenodo.164206. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 303 K. Simulated with CHARMM36 in GROMACS 5.0.6 for 500 ns (32512 atoms). Deposited + as NMRlipids Databank simulation 99 and available from https://doi.org/10.5281/zenodo.164206. sameAs: https://doi.org/10.5281/zenodo.164206 datePublished: '2016-11-01' license: diff --git a/Simulations/bda/dad/bdadad9052cdba579a5d20ad8ca47e47438e3ea0/87fcf2dac21c99fc7af3a31e9fa111d0890b3d61/README.yaml b/Simulations/bda/dad/bdadad9052cdba579a5d20ad8ca47e47438e3ea0/87fcf2dac21c99fc7af3a31e9fa111d0890b3d61/README.yaml index a53a850b8a..a6e427c909 100644 --- a/Simulations/bda/dad/bdadad9052cdba579a5d20ad8ca47e47438e3ea0/87fcf2dac21c99fc7af3a31e9fa111d0890b3d61/README.yaml +++ b/Simulations/bda/dad/bdadad9052cdba579a5d20ad8ca47e47438e3ea0/87fcf2dac21c99fc7af3a31e9fa111d0890b3d61/README.yaml @@ -43,9 +43,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 504 bioschema_properties: - name: Molecular dynamics trajectory of a DOPC bilayer at 313.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 504] + name: Molecular dynamics trajectory of a DOPC bilayer at 313.15 K (CHARMM36, GROMACS, + 1001 ns) [NMRlipids simulation 504] alternateName: 1024DOPC_51200SOL_313K - description: Molecular dynamics trajectory of a lipid bilayer of 1024 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) at 313.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (294912 atoms). Deposited as NMRlipids Databank simulation 504 and available from https://doi.org/10.5281/zenodo.6943086. + description: Molecular dynamics trajectory of a lipid bilayer of 1024 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) + at 313.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (294912 atoms). Deposited + as NMRlipids Databank simulation 504 and available from https://doi.org/10.5281/zenodo.6943086. sameAs: https://doi.org/10.5281/zenodo.6943086 datePublished: '2022-07-30' license: diff --git a/Simulations/bde/036/bde036f1f732e8a257ce442f950948d34dd9497a/60ca3ae5ec8ac67a49f3bcba6cc37d12409489a0/README.yaml b/Simulations/bde/036/bde036f1f732e8a257ce442f950948d34dd9497a/60ca3ae5ec8ac67a49f3bcba6cc37d12409489a0/README.yaml index e7fb9c647f..cab09ddc57 100644 --- a/Simulations/bde/036/bde036f1f732e8a257ce442f950948d34dd9497a/60ca3ae5ec8ac67a49f3bcba6cc37d12409489a0/README.yaml +++ b/Simulations/bde/036/bde036f1f732e8a257ce442f950948d34dd9497a/60ca3ae5ec8ac67a49f3bcba6cc37d12409489a0/README.yaml @@ -43,9 +43,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 325 bioschema_properties: - name: Molecular dynamics trajectory of a DOPC bilayer at 323.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 325] + name: Molecular dynamics trajectory of a DOPC bilayer at 323.15 K (CHARMM36, GROMACS, + 1001 ns) [NMRlipids simulation 325] alternateName: 256DOPC_12800SOL_323K - description: Molecular dynamics trajectory of a lipid bilayer of 256 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) at 323.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (73728 atoms). Deposited as NMRlipids Databank simulation 325 and available from https://doi.org/10.5281/zenodo.6943086. + description: Molecular dynamics trajectory of a lipid bilayer of 256 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) + at 323.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (73728 atoms). Deposited + as NMRlipids Databank simulation 325 and available from https://doi.org/10.5281/zenodo.6943086. sameAs: https://doi.org/10.5281/zenodo.6943086 datePublished: '2022-07-30' license: diff --git a/Simulations/be4/65c/be465ca0eb117d3f878a3c68044c87bd245b0f26/97421e83dc732c3824459532d6fb224a03b78535/README.yaml b/Simulations/be4/65c/be465ca0eb117d3f878a3c68044c87bd245b0f26/97421e83dc732c3824459532d6fb224a03b78535/README.yaml index 50605e8d0f..161a3aa418 100644 --- a/Simulations/be4/65c/be465ca0eb117d3f878a3c68044c87bd245b0f26/97421e83dc732c3824459532d6fb224a03b78535/README.yaml +++ b/Simulations/be4/65c/be465ca0eb117d3f878a3c68044c87bd245b0f26/97421e83dc732c3824459532d6fb224a03b78535/README.yaml @@ -54,9 +54,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 57 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (37:32:32) bilayer at 313 K (ECC-lipids, GROMACS 5.1.4, 300 ns) [NMRlipids simulation 57] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (37:32:32) bilayer at 313 + K (ECC-lipids, GROMACS 5.1.4, 300 ns) [NMRlipids simulation 57] alternateName: 128POPC_6232SOL_110SOD_110CLA_313K - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 37 mol%), 110 CLA (32 mol%) and 110 SOD (32 mol%) at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 300 ns (36068 atoms). Deposited as NMRlipids Databank simulation 57 and available from https://doi.org/10.5281/zenodo.3335503. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 37 mol%), 110 CLA (32 mol%) and 110 SOD (32 mol%) at 313 K. Simulated with ECC-lipids + in GROMACS 5.1.4 for 300 ns (36068 atoms). Deposited as NMRlipids Databank simulation + 57 and available from https://doi.org/10.5281/zenodo.3335503. sameAs: https://doi.org/10.5281/zenodo.3335503 datePublished: '2017-12-19' license: @@ -148,7 +152,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3335503 identifier: 10.5281/zenodo.3335503 url: https://doi.org/10.5281/zenodo.3335503 - name: Simulations of POPC lipid bilayer in water solution at various NaCl, KCl and CaCl2 concentrations using ECC-POPC force field + name: Simulations of POPC lipid bilayer in water solution at various NaCl, KCl + and CaCl2 concentrations using ECC-POPC force field publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/be6/5d5/be65d56aa0b9732c1f75b8e2de40133ac6c5f706/fe08222fa3d4cc603161b05233be0af37dd3cc8b/README.yaml b/Simulations/be6/5d5/be65d56aa0b9732c1f75b8e2de40133ac6c5f706/fe08222fa3d4cc603161b05233be0af37dd3cc8b/README.yaml index 6921babf1b..959162f6ef 100644 --- a/Simulations/be6/5d5/be65d56aa0b9732c1f75b8e2de40133ac6c5f706/fe08222fa3d4cc603161b05233be0af37dd3cc8b/README.yaml +++ b/Simulations/be6/5d5/be65d56aa0b9732c1f75b8e2de40133ac6c5f706/fe08222fa3d4cc603161b05233be0af37dd3cc8b/README.yaml @@ -46,9 +46,13 @@ DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 58 AUTHORS_CONTACT: Kiirikki, M. Anne; Ollila O. H. Samuli bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPG/SOD (67:17:17) bilayer at 298 K (CHARMM36, GROMACS, 300 ns) [NMRlipids simulation 58] + name: Molecular dynamics trajectory of a POPC/POPG/SOD (67:17:17) bilayer at 298 + K (CHARMM36, GROMACS, 300 ns) [NMRlipids simulation 58] alternateName: POPC:POPG(4:1)_T298K - description: Molecular dynamics trajectory of a lipid bilayer of 350 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 67 mol%), 88 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 17 mol%) and 88 SOD (17 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for 300 ns (137004 atoms). Deposited as NMRlipids Databank simulation 58 and available from https://doi.org/10.5281/zenodo.3996952. + description: Molecular dynamics trajectory of a lipid bilayer of 350 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 67 mol%), 88 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 17 mol%) + and 88 SOD (17 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for 300 ns (137004 + atoms). Deposited as NMRlipids Databank simulation 58 and available from https://doi.org/10.5281/zenodo.3996952. sameAs: https://doi.org/10.5281/zenodo.3996952 datePublished: '2020-08-24' license: diff --git a/Simulations/bec/c80/becc80bf8adc6b6d08f7723d2b4653e347a77331/0eb9856aad2baa87438410ae693d18eebe3e8da1/README.yaml b/Simulations/bec/c80/becc80bf8adc6b6d08f7723d2b4653e347a77331/0eb9856aad2baa87438410ae693d18eebe3e8da1/README.yaml index d4804819f4..2181eff09c 100644 --- a/Simulations/bec/c80/becc80bf8adc6b6d08f7723d2b4653e347a77331/0eb9856aad2baa87438410ae693d18eebe3e8da1/README.yaml +++ b/Simulations/bec/c80/becc80bf8adc6b6d08f7723d2b4653e347a77331/0eb9856aad2baa87438410ae693d18eebe3e8da1/README.yaml @@ -40,9 +40,12 @@ EXPERIMENT: FORMFACTOR: - 10.1021/acs.jctc.3c00648/1 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 300 K (FF-development, GROMACS, 288 ns) [NMRlipids simulation 837] + name: Molecular dynamics trajectory of a POPC bilayer at 300 K (FF-development, + GROMACS, 288 ns) [NMRlipids simulation 837] alternateName: POPCandTIP3P - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 300 K. Simulated with FF-development in GROMACS for 288 ns (32512 atoms). Deposited as NMRlipids Databank simulation 837 and available from https://doi.org/10.5281/zenodo.15021844. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 300 K. Simulated with FF-development in GROMACS for 288 ns (32512 atoms). Deposited + as NMRlipids Databank simulation 837 and available from https://doi.org/10.5281/zenodo.15021844. sameAs: https://doi.org/10.5281/zenodo.15021844 datePublished: '2025-03-13' license: diff --git a/Simulations/bf8/3a4/bf83a4c610244ec998461b093c395309dc91837e/bf83a4c610244ec998461b093c395309dc91837e/README.yaml b/Simulations/bf8/3a4/bf83a4c610244ec998461b093c395309dc91837e/bf83a4c610244ec998461b093c395309dc91837e/README.yaml index d1e1145517..eb8bcb90e2 100644 --- a/Simulations/bf8/3a4/bf83a4c610244ec998461b093c395309dc91837e/bf83a4c610244ec998461b093c395309dc91837e/README.yaml +++ b/Simulations/bf8/3a4/bf83a4c610244ec998461b093c395309dc91837e/bf83a4c610244ec998461b093c395309dc91837e/README.yaml @@ -77,9 +77,17 @@ EXPERIMENT: CHOL: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a CHOL/POPC/SM16/POPE/SOD/POPS/SAPI24 (35:19:14:13:12:6:1) bilayer at 310 K (CHARMM36m, NAMD 2.14, 200 ns) [NMRlipids simulation 774] + name: Molecular dynamics trajectory of a CHOL/POPC/SM16/POPE/SOD/POPS/SAPI24 (35:19:14:13:12:6:1) + bilayer at 310 K (CHARMM36m, NAMD 2.14, 200 ns) [NMRlipids simulation 774] alternateName: (innerleaflet,76CHOL,30POPC,52POPE,26POPS,6SAPI24)(outerleaflet,76CHOL,52POPC,6POPE,2POPS,57PSM),13495SOL,52SOD - description: Molecular dynamics trajectory of a lipid bilayer of 152 CHOL (cholesterol, 35 mol%), 82 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 19 mol%), 59 SM16 (N-palmitoyl-D-erythro-sphingosylphosphorylcholine, 14 mol%), 58 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 13 mol%), 52 SOD (12 mol%), 28 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 6 mol%) and 6 SAPI24 (1-stearoyl-2-arachidonoyl-sn-glycero-3-phospho-(1’-myo-inositol-4’,5’-bisphosphate), 1 mol%) at 310 K. Simulated with CHARMM36m in NAMD 2.14 for 200 ns (81972 atoms). Deposited as NMRlipids Databank simulation 774 and available from https://doi.org/10.5281/zenodo.8369348. + description: Molecular dynamics trajectory of a lipid bilayer of 152 CHOL (cholesterol, + 35 mol%), 82 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 19 mol%), + 59 SM16 (N-palmitoyl-D-erythro-sphingosylphosphorylcholine, 14 mol%), 58 POPE + (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 13 mol%), 52 SOD (12 mol%), + 28 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 6 mol%) and 6 SAPI24 + (1-stearoyl-2-arachidonoyl-sn-glycero-3-phospho-(1’-myo-inositol-4’,5’-bisphosphate), + 1 mol%) at 310 K. Simulated with CHARMM36m in NAMD 2.14 for 200 ns (81972 atoms). + Deposited as NMRlipids Databank simulation 774 and available from https://doi.org/10.5281/zenodo.8369348. sameAs: https://doi.org/10.5281/zenodo.8369348 datePublished: '2023-09-18' license: diff --git a/Simulations/bfa/add/bfaadd3db34555a7cb9c66667493f5b534350c7d/3932a021491cd526f760fe7b872b92c780a4cddc/README.yaml b/Simulations/bfa/add/bfaadd3db34555a7cb9c66667493f5b534350c7d/3932a021491cd526f760fe7b872b92c780a4cddc/README.yaml index 3f497a3b16..45f0e478ec 100644 --- a/Simulations/bfa/add/bfaadd3db34555a7cb9c66667493f5b534350c7d/3932a021491cd526f760fe7b872b92c780a4cddc/README.yaml +++ b/Simulations/bfa/add/bfaadd3db34555a7cb9c66667493f5b534350c7d/3932a021491cd526f760fe7b872b92c780a4cddc/README.yaml @@ -40,9 +40,12 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 301 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 303 K (CHARMM36, GROMACS 5.0.6, 500 ns) [NMRlipids simulation 301] + name: Molecular dynamics trajectory of a POPC bilayer at 303 K (CHARMM36, GROMACS + 5.0.6, 500 ns) [NMRlipids simulation 301] alternateName: 128POPC_5120SOL_8A-switch_v4 - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 303 K. Simulated with CHARMM36 in GROMACS 5.0.6 for 500 ns (32512 atoms). Deposited as NMRlipids Databank simulation 301 and available from https://doi.org/10.5281/zenodo.164206. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 303 K. Simulated with CHARMM36 in GROMACS 5.0.6 for 500 ns (32512 atoms). Deposited + as NMRlipids Databank simulation 301 and available from https://doi.org/10.5281/zenodo.164206. sameAs: https://doi.org/10.5281/zenodo.164206 datePublished: '2016-11-01' license: diff --git a/Simulations/bfc/e83/bfce83d9ff8cd12765e2169d49d70ab585376cf7/fa727d520a1de12619020a9beff3ae3fa70f20b1/README.yaml b/Simulations/bfc/e83/bfce83d9ff8cd12765e2169d49d70ab585376cf7/fa727d520a1de12619020a9beff3ae3fa70f20b1/README.yaml index 3262d7f456..df59bf9417 100644 --- a/Simulations/bfc/e83/bfce83d9ff8cd12765e2169d49d70ab585376cf7/fa727d520a1de12619020a9beff3ae3fa70f20b1/README.yaml +++ b/Simulations/bfc/e83/bfce83d9ff8cd12765e2169d49d70ab585376cf7/fa727d520a1de12619020a9beff3ae3fa70f20b1/README.yaml @@ -54,9 +54,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 878 bioschema_properties: - name: Molecular dynamics trajectory of a POPE/NH4/POPI (67:17:17) bilayer at 310 K (CHARMM36, GROMACS 2022.4, 500 ns) [NMRlipids simulation 878] + name: Molecular dynamics trajectory of a POPE/NH4/POPI (67:17:17) bilayer at 310 + K (CHARMM36, GROMACS 2022.4, 500 ns) [NMRlipids simulation 878] alternateName: POPI-POPE (20:80), full hydration, 310 K, NH4+ counter ions - description: Molecular dynamics trajectory of a lipid bilayer of 160 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 67 mol%), 40 NH4 (17 mol%) and 40 POPI (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoinositol, 17 mol%) at 310 K. Simulated with CHARMM36 in GROMACS 2022.4 for 500 ns (55680 atoms). Deposited as NMRlipids Databank simulation 878 and available from https://doi.org/10.5281/zenodo.10280829. + description: Molecular dynamics trajectory of a lipid bilayer of 160 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, + 67 mol%), 40 NH4 (17 mol%) and 40 POPI (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoinositol, + 17 mol%) at 310 K. Simulated with CHARMM36 in GROMACS 2022.4 for 500 ns (55680 + atoms). Deposited as NMRlipids Databank simulation 878 and available from https://doi.org/10.5281/zenodo.10280829. sameAs: https://doi.org/10.5281/zenodo.10280829 datePublished: '2023-12-18' license: diff --git a/Simulations/bff/03d/bff03d4634b72a5467fa6dc5b67767a764db0931/00efd2d1108a76498201aecd69f82d12efc0368a/README.yaml b/Simulations/bff/03d/bff03d4634b72a5467fa6dc5b67767a764db0931/00efd2d1108a76498201aecd69f82d12efc0368a/README.yaml index 92f06f8635..0becb11eda 100644 --- a/Simulations/bff/03d/bff03d4634b72a5467fa6dc5b67767a764db0931/00efd2d1108a76498201aecd69f82d12efc0368a/README.yaml +++ b/Simulations/bff/03d/bff03d4634b72a5467fa6dc5b67767a764db0931/00efd2d1108a76498201aecd69f82d12efc0368a/README.yaml @@ -43,9 +43,12 @@ EXPERIMENT: - 10.1103.008/PhysRevE.80.021931/2 ID: 820 bioschema_properties: - name: Molecular dynamics trajectory of a SOPC bilayer at 303.15 K (CHARMM36, GROMACS 2022.5, 500 ns) [NMRlipids simulation 820] + name: Molecular dynamics trajectory of a SOPC bilayer at 303.15 K (CHARMM36, GROMACS + 2022.5, 500 ns) [NMRlipids simulation 820] alternateName: SOPC - description: Molecular dynamics trajectory of a lipid bilayer of 64 SOPC (1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 303.15 K. Simulated with CHARMM36 in GROMACS 2022.5 for 500 ns (18560 atoms). Deposited as NMRlipids Databank simulation 820 and available from https://doi.org/10.5281/zenodo.12698832. + description: Molecular dynamics trajectory of a lipid bilayer of 64 SOPC (1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 303.15 K. Simulated with CHARMM36 in GROMACS 2022.5 for 500 ns (18560 atoms). + Deposited as NMRlipids Databank simulation 820 and available from https://doi.org/10.5281/zenodo.12698832. sameAs: https://doi.org/10.5281/zenodo.12698832 datePublished: '2024-07-09' license: diff --git a/Simulations/c04/cdb/c04cdb61143bb72ba2ddee11599e6bbfaf6cb211/a31f42800216d84d2242eae2af8ac2cbd6b033ee/README.yaml b/Simulations/c04/cdb/c04cdb61143bb72ba2ddee11599e6bbfaf6cb211/a31f42800216d84d2242eae2af8ac2cbd6b033ee/README.yaml index e1f03ad074..d4f6bdb760 100644 --- a/Simulations/c04/cdb/c04cdb61143bb72ba2ddee11599e6bbfaf6cb211/a31f42800216d84d2242eae2af8ac2cbd6b033ee/README.yaml +++ b/Simulations/c04/cdb/c04cdb61143bb72ba2ddee11599e6bbfaf6cb211/a31f42800216d84d2242eae2af8ac2cbd6b033ee/README.yaml @@ -37,9 +37,12 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/1 ID: 829 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 300 K (Sage 2.2.1, GROMACS, 500 ns) [NMRlipids simulation 829] + name: Molecular dynamics trajectory of a POPC bilayer at 300 K (Sage 2.2.1, GROMACS, + 500 ns) [NMRlipids simulation 829] alternateName: POPCandTIP3P - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 300 K. Simulated with Sage 2.2.1 in GROMACS for 500 ns (32512 atoms). Deposited as NMRlipids Databank simulation 829 and available from https://doi.org/10.5281/zenodo.14713793. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 300 K. Simulated with Sage 2.2.1 in GROMACS for 500 ns (32512 atoms). Deposited + as NMRlipids Databank simulation 829 and available from https://doi.org/10.5281/zenodo.14713793. sameAs: https://doi.org/10.5281/zenodo.14713793 datePublished: '2025-01-21' license: diff --git a/Simulations/c17/59d/c1759dd2351b303be2f9acde5b8e9dcd7eaf22b1/9e4948f45157c1c4efd364b200f56b244d29e012/README.yaml b/Simulations/c17/59d/c1759dd2351b303be2f9acde5b8e9dcd7eaf22b1/9e4948f45157c1c4efd364b200f56b244d29e012/README.yaml index 74cbb21301..5cbcba991c 100644 --- a/Simulations/c17/59d/c1759dd2351b303be2f9acde5b8e9dcd7eaf22b1/9e4948f45157c1c4efd364b200f56b244d29e012/README.yaml +++ b/Simulations/c17/59d/c1759dd2351b303be2f9acde5b8e9dcd7eaf22b1/9e4948f45157c1c4efd364b200f56b244d29e012/README.yaml @@ -51,9 +51,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/3 ID: 426 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (89:11) bilayer at 298.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 426] + name: Molecular dynamics trajectory of a POPC/CHOL (89:11) bilayer at 298.15 K (CHARMM36, + GROMACS, 1001 ns) [NMRlipids simulation 426] alternateName: 1024POPC_128CHOL_57600SOL_298K - description: Molecular dynamics trajectory of a lipid bilayer of 1024 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 89 mol%) and 128 CHOL (cholesterol, 11 mol%) at 298.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (319488 atoms). Deposited as NMRlipids Databank simulation 426 and available from https://doi.org/10.5281/zenodo.5767451. + description: Molecular dynamics trajectory of a lipid bilayer of 1024 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 89 mol%) and 128 CHOL (cholesterol, 11 mol%) at 298.15 K. Simulated with CHARMM36 + in GROMACS for 1001 ns (319488 atoms). Deposited as NMRlipids Databank simulation + 426 and available from https://doi.org/10.5281/zenodo.5767451. sameAs: https://doi.org/10.5281/zenodo.5767451 datePublished: '2021-12-08' license: diff --git a/Simulations/c1c/7e8/c1c7e87cdd750e3f3cac287b1ec9a7b8a3073e7f/3a06317a55c1d39806ba7c612ac639017c4b5245/README.yaml b/Simulations/c1c/7e8/c1c7e87cdd750e3f3cac287b1ec9a7b8a3073e7f/3a06317a55c1d39806ba7c612ac639017c4b5245/README.yaml index 96446853fb..664059fd58 100644 --- a/Simulations/c1c/7e8/c1c7e87cdd750e3f3cac287b1ec9a7b8a3073e7f/3a06317a55c1d39806ba7c612ac639017c4b5245/README.yaml +++ b/Simulations/c1c/7e8/c1c7e87cdd750e3f3cac287b1ec9a7b8a3073e7f/3a06317a55c1d39806ba7c612ac639017c4b5245/README.yaml @@ -43,9 +43,12 @@ ID: 812 WARNINGS: PBC: z-jumps bioschema_properties: - name: Molecular dynamics trajectory of a DMPC bilayer at 314 K (OPLS4, GROMACS Desmond 2022-2, 490 ns) [NMRlipids simulation 812] + name: Molecular dynamics trajectory of a DMPC bilayer at 314 K (OPLS4, GROMACS Desmond + 2022-2, 490 ns) [NMRlipids simulation 812] alternateName: 200DMPC_4000SOL_300K - description: Molecular dynamics trajectory of a lipid bilayer of 200 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) at 314 K. Simulated with OPLS4 in GROMACS Desmond 2022-2 for 490 ns (35600 atoms). Deposited as NMRlipids Databank simulation 812 and available from https://doi.org/10.5281/zenodo.11044799. + description: Molecular dynamics trajectory of a lipid bilayer of 200 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) + at 314 K. Simulated with OPLS4 in GROMACS Desmond 2022-2 for 490 ns (35600 atoms). + Deposited as NMRlipids Databank simulation 812 and available from https://doi.org/10.5281/zenodo.11044799. sameAs: https://doi.org/10.5281/zenodo.11044799 datePublished: '2024-04-23' license: diff --git a/Simulations/c1e/7b5/c1e7b598ab8e55ac5043c26df9fcb3f4e2fd179e/f7af73e8235697c4e9526dcf09960ccb774ba382/README.yaml b/Simulations/c1e/7b5/c1e7b598ab8e55ac5043c26df9fcb3f4e2fd179e/f7af73e8235697c4e9526dcf09960ccb774ba382/README.yaml index 6d9e007fd6..365c32ffd9 100644 --- a/Simulations/c1e/7b5/c1e7b598ab8e55ac5043c26df9fcb3f4e2fd179e/f7af73e8235697c4e9526dcf09960ccb774ba382/README.yaml +++ b/Simulations/c1e/7b5/c1e7b598ab8e55ac5043c26df9fcb3f4e2fd179e/f7af73e8235697c4e9526dcf09960ccb774ba382/README.yaml @@ -48,9 +48,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 351 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (39:31:31) bilayer at 310.15 K (ECC-CHARMM36, GROMACS 5.1.4, 352 ns) [NMRlipids simulation 351] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (39:31:31) bilayer at 310.15 + K (ECC-CHARMM36, GROMACS 5.1.4, 352 ns) [NMRlipids simulation 351] alternateName: 200POPC_9000SOL_157SOD_157CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 39 mol%), 157 CLA (31 mol%) and 157 SOD (31 mol%) at 310.15 K. Simulated with ECC-CHARMM36 in GROMACS 5.1.4 for 352 ns (54114 atoms). Deposited as NMRlipids Databank simulation 351 and available from https://doi.org/10.5281/zenodo.2562083. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 39 mol%), 157 CLA (31 mol%) and 157 SOD (31 mol%) at 310.15 K. Simulated with + ECC-CHARMM36 in GROMACS 5.1.4 for 352 ns (54114 atoms). Deposited as NMRlipids + Databank simulation 351 and available from https://doi.org/10.5281/zenodo.2562083. sameAs: https://doi.org/10.5281/zenodo.2562083 datePublished: '2019-02-11' license: @@ -138,7 +142,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.2562083 identifier: 10.5281/zenodo.2562083 url: https://doi.org/10.5281/zenodo.2562083 - name: Simulation data for ECC-CHARMM36 POPC bilayer, 100 lipids/leaflet, 940 mM NaCl, 310K, GROMACS 5.1.4 + name: Simulation data for ECC-CHARMM36 POPC bilayer, 100 lipids/leaflet, 940 mM + NaCl, 310K, GROMACS 5.1.4 publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/c2e/f1a/c2ef1afc8f1377e0bc9039a69a9831c8aa471d6e/62c50ba947db010b01e3a12321ded513ad4dde2f/README.yaml b/Simulations/c2e/f1a/c2ef1afc8f1377e0bc9039a69a9831c8aa471d6e/62c50ba947db010b01e3a12321ded513ad4dde2f/README.yaml index 41ad26c071..0473c93f61 100644 --- a/Simulations/c2e/f1a/c2ef1afc8f1377e0bc9039a69a9831c8aa471d6e/62c50ba947db010b01e3a12321ded513ad4dde2f/README.yaml +++ b/Simulations/c2e/f1a/c2ef1afc8f1377e0bc9039a69a9831c8aa471d6e/62c50ba947db010b01e3a12321ded513ad4dde2f/README.yaml @@ -55,9 +55,14 @@ EXPERIMENT: POPE: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a POPC/SOD/POPE/TOCL (33:33:17:17) bilayer at 310 K (Charmm36, GROMACS, 570 ns) [NMRlipids simulation 787] + name: Molecular dynamics trajectory of a POPC/SOD/POPE/TOCL (33:33:17:17) bilayer + at 310 K (Charmm36, GROMACS, 570 ns) [NMRlipids simulation 787] alternateName: POPC/POPE/TOCL mixture - description: Molecular dynamics trajectory of a lipid bilayer of 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 33 mol%), 60 SOD (33 mol%), 30 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 17 mol%) and 30 TOCL (1’,3’-Bis[1,2-dioleoyl-sn-glycero-3-phospho]-glycerol, 17 mol%) at 310 K. Simulated with Charmm36 in GROMACS for 570 ns (46290 atoms). Deposited as NMRlipids Databank simulation 787 and available from https://doi.org/10.5281/zenodo.13984187. + description: Molecular dynamics trajectory of a lipid bilayer of 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 33 mol%), 60 SOD (33 mol%), 30 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, + 17 mol%) and 30 TOCL (1’,3’-Bis[1,2-dioleoyl-sn-glycero-3-phospho]-glycerol, 17 + mol%) at 310 K. Simulated with Charmm36 in GROMACS for 570 ns (46290 atoms). Deposited + as NMRlipids Databank simulation 787 and available from https://doi.org/10.5281/zenodo.13984187. sameAs: https://doi.org/10.5281/zenodo.13984187 datePublished: '2023-09-29' license: diff --git a/Simulations/c2f/cb0/c2fcb067df2e1da3432eff195988b7213da19e4f/e1accdc68e32ff10512badff0fb466be197b4534/README.yaml b/Simulations/c2f/cb0/c2fcb067df2e1da3432eff195988b7213da19e4f/e1accdc68e32ff10512badff0fb466be197b4534/README.yaml index 5ff0668e63..1857d54340 100644 --- a/Simulations/c2f/cb0/c2fcb067df2e1da3432eff195988b7213da19e4f/e1accdc68e32ff10512badff0fb466be197b4534/README.yaml +++ b/Simulations/c2f/cb0/c2fcb067df2e1da3432eff195988b7213da19e4f/e1accdc68e32ff10512badff0fb466be197b4534/README.yaml @@ -39,9 +39,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 446 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 310 K (MacRog, GROMACS 4.6.3, 80 ns) [NMRlipids simulation 446] + name: Molecular dynamics trajectory of a POPC bilayer at 310 K (MacRog, GROMACS + 4.6.3, 80 ns) [NMRlipids simulation 446] alternateName: 288POPC_12600SOL_310K - description: Molecular dynamics trajectory of a lipid bilayer of 288 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 310 K. Simulated with MacRog in GROMACS 4.6.3 for 80 ns (76392 atoms). Deposited as NMRlipids Databank simulation 446 and available from https://doi.org/10.5281/zenodo.13497. + description: Molecular dynamics trajectory of a lipid bilayer of 288 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 310 K. Simulated with MacRog in GROMACS 4.6.3 for 80 ns (76392 atoms). Deposited + as NMRlipids Databank simulation 446 and available from https://doi.org/10.5281/zenodo.13497. sameAs: https://doi.org/10.5281/zenodo.13497 datePublished: '2014-12-30' license: diff --git a/Simulations/c3a/32e/c3a32e93b4713c8064ab4c5a998e56194927e0b1/30503ef30485f19bc2465c1245a1cf26de892fe5/README.yaml b/Simulations/c3a/32e/c3a32e93b4713c8064ab4c5a998e56194927e0b1/30503ef30485f19bc2465c1245a1cf26de892fe5/README.yaml index b64607d2fa..54956524b6 100644 --- a/Simulations/c3a/32e/c3a32e93b4713c8064ab4c5a998e56194927e0b1/30503ef30485f19bc2465c1245a1cf26de892fe5/README.yaml +++ b/Simulations/c3a/32e/c3a32e93b4713c8064ab4c5a998e56194927e0b1/30503ef30485f19bc2465c1245a1cf26de892fe5/README.yaml @@ -43,9 +43,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 104 bioschema_properties: - name: Molecular dynamics trajectory of a DOPC bilayer at 323.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 104] + name: Molecular dynamics trajectory of a DOPC bilayer at 323.15 K (CHARMM36, GROMACS, + 1001 ns) [NMRlipids simulation 104] alternateName: 1024DOPC_51200SOL_323K - description: Molecular dynamics trajectory of a lipid bilayer of 1024 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) at 323.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (294912 atoms). Deposited as NMRlipids Databank simulation 104 and available from https://doi.org/10.5281/zenodo.6943086. + description: Molecular dynamics trajectory of a lipid bilayer of 1024 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) + at 323.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (294912 atoms). Deposited + as NMRlipids Databank simulation 104 and available from https://doi.org/10.5281/zenodo.6943086. sameAs: https://doi.org/10.5281/zenodo.6943086 datePublished: '2022-07-30' license: diff --git a/Simulations/c3a/a7c/c3aa7c2c4a5525fddd47307596cc5c1b1efac493/14dabed039416848fd0ccaaf8c8de4ae4acac631/README.yaml b/Simulations/c3a/a7c/c3aa7c2c4a5525fddd47307596cc5c1b1efac493/14dabed039416848fd0ccaaf8c8de4ae4acac631/README.yaml index 98e9f66178..83b868f183 100644 --- a/Simulations/c3a/a7c/c3aa7c2c4a5525fddd47307596cc5c1b1efac493/14dabed039416848fd0ccaaf8c8de4ae4acac631/README.yaml +++ b/Simulations/c3a/a7c/c3aa7c2c4a5525fddd47307596cc5c1b1efac493/14dabed039416848fd0ccaaf8c8de4ae4acac631/README.yaml @@ -40,9 +40,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 818 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 300 K (Charmm36, GROMACS 2019.5, 425 ns) [NMRlipids simulation 818] + name: Molecular dynamics trajectory of a POPC bilayer at 300 K (Charmm36, GROMACS + 2019.5, 425 ns) [NMRlipids simulation 818] alternateName: POPС(300K, 10w/l, CHARMM36) - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 300 K. Simulated with Charmm36 in GROMACS 2019.5 for 425 ns (32800 atoms). Deposited as NMRlipids Databank simulation 818 and available from https://doi.org/10.5281/zenodo.6334005. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 300 K. Simulated with Charmm36 in GROMACS 2019.5 for 425 ns (32800 atoms). + Deposited as NMRlipids Databank simulation 818 and available from https://doi.org/10.5281/zenodo.6334005. sameAs: https://doi.org/10.5281/zenodo.6334005 datePublished: '2022-03-07' license: diff --git a/Simulations/c3b/ff6/c3bff6e99c4e8c010bf13671f7aae6df192e12e7/fd6f540f5f44d50bfc059c16ce23db6666eb7810/README.yaml b/Simulations/c3b/ff6/c3bff6e99c4e8c010bf13671f7aae6df192e12e7/fd6f540f5f44d50bfc059c16ce23db6666eb7810/README.yaml index 9728a9a088..7cc82adb07 100644 --- a/Simulations/c3b/ff6/c3bff6e99c4e8c010bf13671f7aae6df192e12e7/fd6f540f5f44d50bfc059c16ce23db6666eb7810/README.yaml +++ b/Simulations/c3b/ff6/c3bff6e99c4e8c010bf13671f7aae6df192e12e7/fd6f540f5f44d50bfc059c16ce23db6666eb7810/README.yaml @@ -57,9 +57,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 165 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD/CER (72:11:11:7) bilayer at 310 K (CHARMM36, GROMACS 2016.2, 1070 ns) [NMRlipids simulation 165] + name: Molecular dynamics trajectory of a POPC/CLA/SOD/CER (72:11:11:7) bilayer at + 310 K (CHARMM36, GROMACS 2016.2, 1070 ns) [NMRlipids simulation 165] alternateName: 512POPC_50CER_28100SOL_75SOD_75CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 512 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 72 mol%), 75 CLA (11 mol%), 75 SOD (11 mol%) and 50 CER (N-palmitoyl-D-erythro-sphingosine, 7 mol%) at 310 K. Simulated with CHARMM36 in GROMACS 2016.2 for 1070 ns (158308 atoms). Deposited as NMRlipids Databank simulation 165 and available from https://doi.org/10.5281/zenodo.1219494. + description: Molecular dynamics trajectory of a lipid bilayer of 512 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 72 mol%), 75 CLA (11 mol%), 75 SOD (11 mol%) and 50 CER (N-palmitoyl-D-erythro-sphingosine, + 7 mol%) at 310 K. Simulated with CHARMM36 in GROMACS 2016.2 for 1070 ns (158308 + atoms). Deposited as NMRlipids Databank simulation 165 and available from https://doi.org/10.5281/zenodo.1219494. sameAs: https://doi.org/10.5281/zenodo.1219494 datePublished: '2018-04-17' license: diff --git a/Simulations/c3d/47f/c3d47f84c24d1aef48e212cb258e6e54d63404b8/79855c9911fcce258ddc511b9c476b7bfe4c2182/README.yaml b/Simulations/c3d/47f/c3d47f84c24d1aef48e212cb258e6e54d63404b8/79855c9911fcce258ddc511b9c476b7bfe4c2182/README.yaml index 04c36d38a4..747d24a93a 100644 --- a/Simulations/c3d/47f/c3d47f84c24d1aef48e212cb258e6e54d63404b8/79855c9911fcce258ddc511b9c476b7bfe4c2182/README.yaml +++ b/Simulations/c3d/47f/c3d47f84c24d1aef48e212cb258e6e54d63404b8/79855c9911fcce258ddc511b9c476b7bfe4c2182/README.yaml @@ -51,9 +51,14 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 341 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPG/SOD (54:23:23) bilayer at 310 K (CHARMM36 and CHARMM TIP3P, GROMACS 2018.3, 100 ns) [NMRlipids simulation 341] + name: Molecular dynamics trajectory of a POPC/POPG/SOD (54:23:23) bilayer at 310 + K (CHARMM36 and CHARMM TIP3P, GROMACS 2018.3, 100 ns) [NMRlipids simulation 341] alternateName: 350POPC_150POPG_25000SOL_150SOD_310K_1 - description: Molecular dynamics trajectory of a lipid bilayer of 350 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 54 mol%), 150 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 23 mol%) and 150 SOD (23 mol%) at 310 K. Simulated with CHARMM36 and CHARMM TIP3P in GROMACS 2018.3 for 100 ns (141100 atoms). Deposited as NMRlipids Databank simulation 341 and available from https://doi.org/10.5281/zenodo.3248689. + description: Molecular dynamics trajectory of a lipid bilayer of 350 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 54 mol%), 150 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 23 mol%) + and 150 SOD (23 mol%) at 310 K. Simulated with CHARMM36 and CHARMM TIP3P in GROMACS + 2018.3 for 100 ns (141100 atoms). Deposited as NMRlipids Databank simulation 341 + and available from https://doi.org/10.5281/zenodo.3248689. sameAs: https://doi.org/10.5281/zenodo.3248689 datePublished: '2019-06-18' license: diff --git a/Simulations/c3e/a0b/c3ea0bd34198ac22edbce9ea2d1631b495965dfa/5522ba0e97d92d0ad6ca074e7e441efb3d0a6481/README.yaml b/Simulations/c3e/a0b/c3ea0bd34198ac22edbce9ea2d1631b495965dfa/5522ba0e97d92d0ad6ca074e7e441efb3d0a6481/README.yaml index c83fde92e4..eb4f4a0969 100644 --- a/Simulations/c3e/a0b/c3ea0bd34198ac22edbce9ea2d1631b495965dfa/5522ba0e97d92d0ad6ca074e7e441efb3d0a6481/README.yaml +++ b/Simulations/c3e/a0b/c3ea0bd34198ac22edbce9ea2d1631b495965dfa/5522ba0e97d92d0ad6ca074e7e441efb3d0a6481/README.yaml @@ -45,9 +45,12 @@ EXPERIMENT: - 10.1016/j.bbamem.2011.07.022/11 ID: 127 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 313 K (ECC-lipids, GROMACS 5.1.4, 200 ns) [NMRlipids simulation 127] + name: Molecular dynamics trajectory of a POPC bilayer at 313 K (ECC-lipids, GROMACS + 5.1.4, 200 ns) [NMRlipids simulation 127] alternateName: 128POPC_6400SOL_313K_OPC4model - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 200 ns (42752 atoms). Deposited as NMRlipids Databank simulation 127 and available from https://doi.org/10.5281/zenodo.1118980. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 200 ns (42752 atoms). + Deposited as NMRlipids Databank simulation 127 and available from https://doi.org/10.5281/zenodo.1118980. sameAs: https://doi.org/10.5281/zenodo.1118980 datePublished: '2017-12-19' license: @@ -137,7 +140,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1118980 identifier: 10.5281/zenodo.1118980 url: https://doi.org/10.5281/zenodo.1118980 - name: Simulations Of Popc Lipid Bilayer In Water Solution At Various Nacl And Cacl2 Concentrations Using Ecc-Popc Force Field And Various Water Models + name: Simulations Of Popc Lipid Bilayer In Water Solution At Various Nacl And + Cacl2 Concentrations Using Ecc-Popc Force Field And Various Water Models publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/c3f/028/c3f028c4e9ea5847cc395d4f40ce6acf68efda32/496930b1c06fc484c4103b90e8302534f85f9372/README.yaml b/Simulations/c3f/028/c3f028c4e9ea5847cc395d4f40ce6acf68efda32/496930b1c06fc484c4103b90e8302534f85f9372/README.yaml index 40ca46f4c5..a3b202ba42 100644 --- a/Simulations/c3f/028/c3f028c4e9ea5847cc395d4f40ce6acf68efda32/496930b1c06fc484c4103b90e8302534f85f9372/README.yaml +++ b/Simulations/c3f/028/c3f028c4e9ea5847cc395d4f40ce6acf68efda32/496930b1c06fc484c4103b90e8302534f85f9372/README.yaml @@ -45,9 +45,12 @@ ID: 813 WARNINGS: PBC: z-jumps bioschema_properties: - name: Molecular dynamics trajectory of a DMPC bilayer at 314 K (OPLS4, GROMACS Desmond 2022-2, 500 ns) [NMRlipids simulation 813] + name: Molecular dynamics trajectory of a DMPC bilayer at 314 K (OPLS4, GROMACS Desmond + 2022-2, 500 ns) [NMRlipids simulation 813] alternateName: 200DMPC_9000SOL_300K - description: Molecular dynamics trajectory of a lipid bilayer of 200 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) at 314 K. Simulated with OPLS4 in GROMACS Desmond 2022-2 for 500 ns (50600 atoms). Deposited as NMRlipids Databank simulation 813 and available from https://doi.org/10.5281/zenodo.11044615. + description: Molecular dynamics trajectory of a lipid bilayer of 200 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) + at 314 K. Simulated with OPLS4 in GROMACS Desmond 2022-2 for 500 ns (50600 atoms). + Deposited as NMRlipids Databank simulation 813 and available from https://doi.org/10.5281/zenodo.11044615. sameAs: https://doi.org/10.5281/zenodo.11044615 datePublished: '2024-04-23' license: diff --git a/Simulations/c43/6f4/c436f42cfbf0bb88f186b19e35d4e8d19e1812f1/b8719385a1f6d3e6b60785ac2548f154b55ba296/README.yaml b/Simulations/c43/6f4/c436f42cfbf0bb88f186b19e35d4e8d19e1812f1/b8719385a1f6d3e6b60785ac2548f154b55ba296/README.yaml index 209386c53a..a63a088655 100644 --- a/Simulations/c43/6f4/c436f42cfbf0bb88f186b19e35d4e8d19e1812f1/b8719385a1f6d3e6b60785ac2548f154b55ba296/README.yaml +++ b/Simulations/c43/6f4/c436f42cfbf0bb88f186b19e35d4e8d19e1812f1/b8719385a1f6d3e6b60785ac2548f154b55ba296/README.yaml @@ -45,9 +45,12 @@ EXPERIMENT: - 10.1016/j.bbamem.2011.07.022/20 ID: 510 bioschema_properties: - name: Molecular dynamics trajectory of a DMPC bilayer at 333.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 510] + name: Molecular dynamics trajectory of a DMPC bilayer at 333.15 K (CHARMM36, GROMACS, + 1001 ns) [NMRlipids simulation 510] alternateName: 64DMPC_3200SOL_333K - description: Molecular dynamics trajectory of a lipid bilayer of 64 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (17152 atoms). Deposited as NMRlipids Databank simulation 510 and available from https://doi.org/10.5281/zenodo.6943413. + description: Molecular dynamics trajectory of a lipid bilayer of 64 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) + at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (17152 atoms). Deposited + as NMRlipids Databank simulation 510 and available from https://doi.org/10.5281/zenodo.6943413. sameAs: https://doi.org/10.5281/zenodo.6943413 datePublished: '2022-07-30' license: @@ -137,7 +140,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.6943413 identifier: 10.5281/zenodo.6943413 url: https://doi.org/10.5281/zenodo.6943413 - name: Simulations of different single-component bilayers, three different system sizes + name: Simulations of different single-component bilayers, three different system + sizes publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/c49/f73/c49f7373e5f014e7249177961c883f238e0ff95e/76053cce890ea85324bb74b299f63432f91f531b/README.yaml b/Simulations/c49/f73/c49f7373e5f014e7249177961c883f238e0ff95e/76053cce890ea85324bb74b299f63432f91f531b/README.yaml index cd4a3e6839..db82a46c82 100644 --- a/Simulations/c49/f73/c49f7373e5f014e7249177961c883f238e0ff95e/76053cce890ea85324bb74b299f63432f91f531b/README.yaml +++ b/Simulations/c49/f73/c49f7373e5f014e7249177961c883f238e0ff95e/76053cce890ea85324bb74b299f63432f91f531b/README.yaml @@ -52,9 +52,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/5 ID: 88 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (80:20) bilayer at 298.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 88] + name: Molecular dynamics trajectory of a POPC/CHOL (80:20) bilayer at 298.15 K (CHARMM36, + GROMACS, 1001 ns) [NMRlipids simulation 88] alternateName: 1024POPC_256CHOL_64000SOL_298K - description: Molecular dynamics trajectory of a lipid bilayer of 1024 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 80 mol%) and 256 CHOL (cholesterol, 20 mol%) at 298.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (348160 atoms). Deposited as NMRlipids Databank simulation 88 and available from https://doi.org/10.5281/zenodo.5767451. + description: Molecular dynamics trajectory of a lipid bilayer of 1024 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 80 mol%) and 256 CHOL (cholesterol, 20 mol%) at 298.15 K. Simulated with CHARMM36 + in GROMACS for 1001 ns (348160 atoms). Deposited as NMRlipids Databank simulation + 88 and available from https://doi.org/10.5281/zenodo.5767451. sameAs: https://doi.org/10.5281/zenodo.5767451 datePublished: '2021-12-08' license: diff --git a/Simulations/c4c/487/c4c4872c6b390f70261dbe916557397e7ac04796/2f2177c61a960beea2dbde7afe74d344c2c16f58/README.yaml b/Simulations/c4c/487/c4c4872c6b390f70261dbe916557397e7ac04796/2f2177c61a960beea2dbde7afe74d344c2c16f58/README.yaml index 0e2c0f9d3f..2e012e9357 100644 --- a/Simulations/c4c/487/c4c4872c6b390f70261dbe916557397e7ac04796/2f2177c61a960beea2dbde7afe74d344c2c16f58/README.yaml +++ b/Simulations/c4c/487/c4c4872c6b390f70261dbe916557397e7ac04796/2f2177c61a960beea2dbde7afe74d344c2c16f58/README.yaml @@ -42,9 +42,12 @@ SOFTWARE: gromacs DIR_WRK: /usr/home/bort/Databank ID: 613 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 310 K (CHARMM36, GROMACS 5.0.4, 500 ns) [NMRlipids simulation 613] + name: Molecular dynamics trajectory of a POPC bilayer at 310 K (CHARMM36, GROMACS + 5.0.4, 500 ns) [NMRlipids simulation 613] alternateName: 72POPC_2880SOL_310K - description: Molecular dynamics trajectory of a lipid bilayer of 72 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 310 K. Simulated with CHARMM36 in GROMACS 5.0.4 for 500 ns (18288 atoms). Deposited as NMRlipids Databank simulation 613 and available from https://doi.org/10.5281/zenodo.1009607. + description: Molecular dynamics trajectory of a lipid bilayer of 72 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 310 K. Simulated with CHARMM36 in GROMACS 5.0.4 for 500 ns (18288 atoms). Deposited + as NMRlipids Databank simulation 613 and available from https://doi.org/10.5281/zenodo.1009607. sameAs: https://doi.org/10.5281/zenodo.1009607 datePublished: '2017-10-12' license: @@ -137,7 +140,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1009607 identifier: 10.5281/zenodo.1009607 url: https://doi.org/10.5281/zenodo.1009607 - name: Set Simulations Small Pure Bilayers (72 Lipids) Using Charmm36 Ff In Gromacs (Dppc, Popc) + name: Set Simulations Small Pure Bilayers (72 Lipids) Using Charmm36 Ff In Gromacs + (Dppc, Popc) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/c4e/397/c4e3979e2f256025713e625bac872e39b9333735/dee62d31f49ab18da7c2966ddb8d439d3fa77072/README.yaml b/Simulations/c4e/397/c4e3979e2f256025713e625bac872e39b9333735/dee62d31f49ab18da7c2966ddb8d439d3fa77072/README.yaml index 1cc4b6c510..d048ae40af 100644 --- a/Simulations/c4e/397/c4e3979e2f256025713e625bac872e39b9333735/dee62d31f49ab18da7c2966ddb8d439d3fa77072/README.yaml +++ b/Simulations/c4e/397/c4e3979e2f256025713e625bac872e39b9333735/dee62d31f49ab18da7c2966ddb8d439d3fa77072/README.yaml @@ -46,9 +46,12 @@ EXPERIMENT: - 10.1016/j.bbamem.2011.07.022/19 ID: 147 bioschema_properties: - name: Molecular dynamics trajectory of a DMPC bilayer at 323 K (Berger lipids + Gromos 53A6, GROMACS, 200 ns) [NMRlipids simulation 147] + name: Molecular dynamics trajectory of a DMPC bilayer at 323 K (Berger lipids + + Gromos 53A6, GROMACS, 200 ns) [NMRlipids simulation 147] alternateName: 128DMPC_3655SOL_323K - description: Molecular dynamics trajectory of a lipid bilayer of 128 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) at 323 K. Simulated with Berger lipids + Gromos 53A6 in GROMACS for 200 ns (16853 atoms). Deposited as NMRlipids Databank simulation 147 and available from https://doi.org/10.5281/zenodo.2605546. + description: Molecular dynamics trajectory of a lipid bilayer of 128 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) + at 323 K. Simulated with Berger lipids + Gromos 53A6 in GROMACS for 200 ns (16853 + atoms). Deposited as NMRlipids Databank simulation 147 and available from https://doi.org/10.5281/zenodo.2605546. sameAs: https://doi.org/10.5281/zenodo.2605546 datePublished: '2019-03-25' license: diff --git a/Simulations/c50/10d/c5010d250e713dc1c00c5df64712f3f2c5453b4e/812185b9c21f8859aa480ecc88a811cedac24325/README.yaml b/Simulations/c50/10d/c5010d250e713dc1c00c5df64712f3f2c5453b4e/812185b9c21f8859aa480ecc88a811cedac24325/README.yaml index 9f840debb4..fd7304e85b 100644 --- a/Simulations/c50/10d/c5010d250e713dc1c00c5df64712f3f2c5453b4e/812185b9c21f8859aa480ecc88a811cedac24325/README.yaml +++ b/Simulations/c50/10d/c5010d250e713dc1c00c5df64712f3f2c5453b4e/812185b9c21f8859aa480ecc88a811cedac24325/README.yaml @@ -51,9 +51,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 53 bioschema_properties: - name: Molecular dynamics trajectory of a DEPC/CLA/SOD (81:9:9) bilayer at 310 K (CHARMM36, GROMACS 2019, 500 ns) [NMRlipids simulation 53] + name: Molecular dynamics trajectory of a DEPC/CLA/SOD (81:9:9) bilayer at 310 K + (CHARMM36, GROMACS 2019, 500 ns) [NMRlipids simulation 53] alternateName: 200DEPC_10000SOL_23SOD_23CLA - description: Molecular dynamics trajectory of a lipid bilayer of 200 DEPC (1,2-dierucoyl-sn-glycero-3-phosphocholine, 81 mol%), 23 CLA (9 mol%) and 23 SOD (9 mol%) at 310 K. Simulated with CHARMM36 in GROMACS 2019 for 500 ns (62446 atoms). Deposited as NMRlipids Databank simulation 53 and available from https://doi.org/10.5281/zenodo.3592499. + description: Molecular dynamics trajectory of a lipid bilayer of 200 DEPC (1,2-dierucoyl-sn-glycero-3-phosphocholine, + 81 mol%), 23 CLA (9 mol%) and 23 SOD (9 mol%) at 310 K. Simulated with CHARMM36 + in GROMACS 2019 for 500 ns (62446 atoms). Deposited as NMRlipids Databank simulation + 53 and available from https://doi.org/10.5281/zenodo.3592499. sameAs: https://doi.org/10.5281/zenodo.3592499 datePublished: '2019-12-24' license: diff --git a/Simulations/c50/7fc/c507fc167592f74bcf57753eda69f6906707afc6/34741e2eaeb4030af973881bb7e14fac7069c317/README.yaml b/Simulations/c50/7fc/c507fc167592f74bcf57753eda69f6906707afc6/34741e2eaeb4030af973881bb7e14fac7069c317/README.yaml index e95c0ffb89..1637f1ab53 100644 --- a/Simulations/c50/7fc/c507fc167592f74bcf57753eda69f6906707afc6/34741e2eaeb4030af973881bb7e14fac7069c317/README.yaml +++ b/Simulations/c50/7fc/c507fc167592f74bcf57753eda69f6906707afc6/34741e2eaeb4030af973881bb7e14fac7069c317/README.yaml @@ -55,9 +55,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 52 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (44:37:19) bilayer at 313 K (ECC-lipids, GROMACS 5.1.4, 2 ns) [NMRlipids simulation 52] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (44:37:19) bilayer at 313 + K (ECC-lipids, GROMACS 5.1.4, 2 ns) [NMRlipids simulation 52] alternateName: 128POPC_6400SOL_54CAL_108CLA_313K_OPC4model - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 44 mol%), 108 CLA (37 mol%) and 54 CAL (19 mol%) at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 2 ns (42914 atoms). Deposited as NMRlipids Databank simulation 52 and available from https://doi.org/10.5281/zenodo.1118980. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 44 mol%), 108 CLA (37 mol%) and 54 CAL (19 mol%) at 313 K. Simulated with ECC-lipids + in GROMACS 5.1.4 for 2 ns (42914 atoms). Deposited as NMRlipids Databank simulation + 52 and available from https://doi.org/10.5281/zenodo.1118980. sameAs: https://doi.org/10.5281/zenodo.1118980 datePublished: '2017-12-19' license: @@ -147,7 +151,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1118980 identifier: 10.5281/zenodo.1118980 url: https://doi.org/10.5281/zenodo.1118980 - name: Simulations Of Popc Lipid Bilayer In Water Solution At Various Nacl And Cacl2 Concentrations Using Ecc-Popc Force Field And Various Water Models + name: Simulations Of Popc Lipid Bilayer In Water Solution At Various Nacl And + Cacl2 Concentrations Using Ecc-Popc Force Field And Various Water Models publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/c51/b34/c51b34a37b0fc7a4b522441a10112b28411f80a4/38058dc73d22c28252a892fb9caced8f2220b4bf/README.yaml b/Simulations/c51/b34/c51b34a37b0fc7a4b522441a10112b28411f80a4/38058dc73d22c28252a892fb9caced8f2220b4bf/README.yaml index 0197330c43..66b28bc910 100644 --- a/Simulations/c51/b34/c51b34a37b0fc7a4b522441a10112b28411f80a4/38058dc73d22c28252a892fb9caced8f2220b4bf/README.yaml +++ b/Simulations/c51/b34/c51b34a37b0fc7a4b522441a10112b28411f80a4/38058dc73d22c28252a892fb9caced8f2220b4bf/README.yaml @@ -57,9 +57,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 132 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL/CLA/SOD (61:26:6:6) bilayer at 310 K (Slipids with ECC-scaled ions (Kohagen), GROMACS 4.6, 200 ns) [NMRlipids simulation 132] + name: Molecular dynamics trajectory of a POPC/CHOL/CLA/SOD (61:26:6:6) bilayer at + 310 K (Slipids with ECC-scaled ions (Kohagen), GROMACS 4.6, 200 ns) [NMRlipids + simulation 132] alternateName: 86CHOL_200POPC_9000SOL_21SOD_21CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 61 mol%), 86 CHOL (cholesterol, 26 mol%), 21 CLA (6 mol%) and 21 SOD (6 mol%) at 310 K. Simulated with Slipids with ECC-scaled ions (Kohagen) in GROMACS 4.6 for 200 ns (60206 atoms). Deposited as NMRlipids Databank simulation 132 and available from https://doi.org/10.5281/zenodo.259343. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 61 mol%), 86 CHOL (cholesterol, 26 mol%), 21 CLA (6 mol%) and 21 SOD (6 mol%) + at 310 K. Simulated with Slipids with ECC-scaled ions (Kohagen) in GROMACS 4.6 + for 200 ns (60206 atoms). Deposited as NMRlipids Databank simulation 132 and available + from https://doi.org/10.5281/zenodo.259343. sameAs: https://doi.org/10.5281/zenodo.259343 datePublished: '2017-01-24' license: @@ -149,7 +155,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.259343 identifier: 10.5281/zenodo.259343 url: https://doi.org/10.5281/zenodo.259343 - name: Popc With Varying Amounts Of Cholesterol, 130 Mm Of Nacl. Slipids With Ecc-Scaled Ions + name: Popc With Varying Amounts Of Cholesterol, 130 Mm Of Nacl. Slipids With Ecc-Scaled + Ions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/c52/945/c52945e563e60264ecd5bbddcbeb7a63a1edded0/be7a712869636298c30e8e6f2b59b1c546c5e044/README.yaml b/Simulations/c52/945/c52945e563e60264ecd5bbddcbeb7a63a1edded0/be7a712869636298c30e8e6f2b59b1c546c5e044/README.yaml index b1b36275dc..85062154c3 100644 --- a/Simulations/c52/945/c52945e563e60264ecd5bbddcbeb7a63a1edded0/be7a712869636298c30e8e6f2b59b1c546c5e044/README.yaml +++ b/Simulations/c52/945/c52945e563e60264ecd5bbddcbeb7a63a1edded0/be7a712869636298c30e8e6f2b59b1c546c5e044/README.yaml @@ -40,9 +40,13 @@ EXPERIMENT: C20: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/C20 (86:14) bilayer at 333 K (SLIPIDS, GROMACS, 100 ns) [NMRlipids simulation 886] + name: Molecular dynamics trajectory of a DPPC/C20 (86:14) bilayer at 333 K (SLIPIDS, + GROMACS, 100 ns) [NMRlipids simulation 886] alternateName: DPPC/C20 - description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 86 mol%) and 12 C20 (n-Eicosane, 14 mol%) at 333 K. Simulated with SLIPIDS in GROMACS for 100 ns (13563 atoms). Deposited as NMRlipids Databank simulation 886 and available from https://doi.org/10.5281/zenodo.7572990. + description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 86 mol%) and 12 C20 (n-Eicosane, 14 mol%) at 333 K. Simulated with SLIPIDS in + GROMACS for 100 ns (13563 atoms). Deposited as NMRlipids Databank simulation 886 + and available from https://doi.org/10.5281/zenodo.7572990. sameAs: https://doi.org/10.5281/zenodo.7572990 datePublished: '2023-01-26' license: @@ -134,7 +138,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.7572990 identifier: 10.5281/zenodo.7572990 url: https://doi.org/10.5281/zenodo.7572990 - name: 'MD simulation input files and results for ,,Atomistic MD simulations of n-alkanes in a phospholipid bilayer: CHARMM36 versus Slipids"' + name: 'MD simulation input files and results for ,,Atomistic MD simulations of + n-alkanes in a phospholipid bilayer: CHARMM36 versus Slipids"' publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/c52/945/c52945e563e60264ecd5bbddcbeb7a63a1edded0/f0d5b8342f3bd53ccb933806591012e78a43190a/README.yaml b/Simulations/c52/945/c52945e563e60264ecd5bbddcbeb7a63a1edded0/f0d5b8342f3bd53ccb933806591012e78a43190a/README.yaml index e4ef10a816..273924838f 100644 --- a/Simulations/c52/945/c52945e563e60264ecd5bbddcbeb7a63a1edded0/f0d5b8342f3bd53ccb933806591012e78a43190a/README.yaml +++ b/Simulations/c52/945/c52945e563e60264ecd5bbddcbeb7a63a1edded0/f0d5b8342f3bd53ccb933806591012e78a43190a/README.yaml @@ -45,9 +45,13 @@ EXPERIMENT: C20: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/C20 (86:14) bilayer at 333 K (Slipids, GROMACS 2018.7, 100 ns) [NMRlipids simulation 885] + name: Molecular dynamics trajectory of a DPPC/C20 (86:14) bilayer at 333 K (Slipids, + GROMACS 2018.7, 100 ns) [NMRlipids simulation 885] alternateName: DPPC:C20(72:20)_60C_Slipids - description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 86 mol%) and 12 C20 (n-Eicosane, 14 mol%) at 333 K. Simulated with Slipids in GROMACS 2018.7 for 100 ns (13563 atoms). Deposited as NMRlipids Databank simulation 885 and available from https://doi.org/10.5281/zenodo.7572990. + description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 86 mol%) and 12 C20 (n-Eicosane, 14 mol%) at 333 K. Simulated with Slipids in + GROMACS 2018.7 for 100 ns (13563 atoms). Deposited as NMRlipids Databank simulation + 885 and available from https://doi.org/10.5281/zenodo.7572990. sameAs: https://doi.org/10.5281/zenodo.7572990 datePublished: '2023-01-26' license: @@ -140,7 +144,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.7572990 identifier: 10.5281/zenodo.7572990 url: https://doi.org/10.5281/zenodo.7572990 - name: 'MD simulation input files and results for ,,Atomistic MD simulations of n-alkanes in a phospholipid bilayer: CHARMM36 versus Slipids"' + name: 'MD simulation input files and results for ,,Atomistic MD simulations of + n-alkanes in a phospholipid bilayer: CHARMM36 versus Slipids"' publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/c54/a7f/c54a7fae3f5d01b83d2bdb3d42700185104e05eb/5a9808f2cedaec641ac9f872e539f852c81aa7fc/DPPC_FragmentQuality.json b/Simulations/c54/a7f/c54a7fae3f5d01b83d2bdb3d42700185104e05eb/5a9808f2cedaec641ac9f872e539f852c81aa7fc/DPPC_FragmentQuality.json new file mode 100644 index 0000000000..863fc976c5 --- /dev/null +++ b/Simulations/c54/a7f/c54a7fae3f5d01b83d2bdb3d42700185104e05eb/5a9808f2cedaec641ac9f872e539f852c81aa7fc/DPPC_FragmentQuality.json @@ -0,0 +1 @@ +{"sn-1": NaN, "sn-2": NaN, "headgroup": 0.6337, "total": 0.6337} \ No newline at end of file diff --git a/Simulations/c54/a7f/c54a7fae3f5d01b83d2bdb3d42700185104e05eb/5a9808f2cedaec641ac9f872e539f852c81aa7fc/DPPC_OrderParameters_quality.json b/Simulations/c54/a7f/c54a7fae3f5d01b83d2bdb3d42700185104e05eb/5a9808f2cedaec641ac9f872e539f852c81aa7fc/DPPC_OrderParameters_quality.json new file mode 100644 index 0000000000..be1ccdee91 --- /dev/null +++ b/Simulations/c54/a7f/c54a7fae3f5d01b83d2bdb3d42700185104e05eb/5a9808f2cedaec641ac9f872e539f852c81aa7fc/DPPC_OrderParameters_quality.json @@ -0,0 +1,84 @@ +{ + "10.1021/bi00687a021/1": { + "M_G1C10_M M_G1C10H1_M": NaN, + "M_G1C10_M M_G1C10H2_M": NaN, + "M_G1C11_M M_G1C11H1_M": NaN, + "M_G1C11_M M_G1C11H2_M": NaN, + "M_G1C12_M M_G1C12H1_M": NaN, + "M_G1C12_M 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NaN, + "M_G2C12_M M_G2C12H2_M": NaN, + "M_G2C13_M M_G2C13H1_M": NaN, + "M_G2C13_M M_G2C13H2_M": NaN, + "M_G2C14_M M_G2C14H1_M": NaN, + "M_G2C14_M M_G2C14H2_M": NaN, + "M_G2C15_M M_G2C15H1_M": NaN, + "M_G2C15_M M_G2C15H2_M": NaN, + "M_G2C16_M M_G2C16H1_M": NaN, + "M_G2C16_M M_G2C16H2_M": NaN, + "M_G2C17_M M_G2C17H1_M": NaN, + "M_G2C17_M M_G2C17H2_M": NaN, + "M_G2C17_M M_G2C17H3_M": NaN, + "M_G2C3_M M_G2C3H1_M": NaN, + "M_G2C3_M M_G2C3H2_M": NaN, + "M_G2C4_M M_G2C4H1_M": NaN, + "M_G2C4_M M_G2C4H2_M": NaN, + "M_G2C5_M M_G2C5H1_M": NaN, + "M_G2C5_M M_G2C5H2_M": NaN, + "M_G2C6_M M_G2C6H1_M": NaN, + "M_G2C6_M M_G2C6H2_M": NaN, + "M_G2C7_M M_G2C7H1_M": NaN, + "M_G2C7_M M_G2C7H2_M": NaN, + "M_G2C8_M M_G2C8H1_M": NaN, + "M_G2C8_M M_G2C8H2_M": NaN, + "M_G2C9_M M_G2C9H1_M": NaN, + "M_G2C9_M M_G2C9H2_M": NaN, + "M_G2_M M_G2H1_M": NaN, + "M_G3C4_M M_G3C4H1_M": 0.0474, + "M_G3C4_M M_G3C4H2_M": 0.0432, + "M_G3C5_M M_G3C5H1_M": 0.789, + "M_G3C5_M M_G3C5H2_M": 0.5155, + "M_G3N6C1_M M_G3N6C1H1_M": 0.986, + "M_G3N6C1_M M_G3N6C1H2_M": 0.9858, + "M_G3N6C1_M M_G3N6C1H3_M": 0.9846, + "M_G3N6C2_M M_G3N6C2H1_M": 0.9849, + "M_G3N6C2_M M_G3N6C2H2_M": 0.9861, + "M_G3N6C2_M M_G3N6C2H3_M": 0.9843, + "M_G3N6C3_M M_G3N6C3H1_M": 0.9853, + "M_G3N6C3_M M_G3N6C3H2_M": 0.9859, + "M_G3N6C3_M M_G3N6C3H3_M": 0.9868, + "M_G3_M M_G3H1_M": 0.3769, + "M_G3_M M_G3H2_M": 0.7643 + } +} \ No newline at end of file diff --git a/Simulations/c54/a7f/c54a7fae3f5d01b83d2bdb3d42700185104e05eb/5a9808f2cedaec641ac9f872e539f852c81aa7fc/FormFactorQuality.json b/Simulations/c54/a7f/c54a7fae3f5d01b83d2bdb3d42700185104e05eb/5a9808f2cedaec641ac9f872e539f852c81aa7fc/FormFactorQuality.json new file mode 100644 index 0000000000..5384d18279 --- /dev/null +++ b/Simulations/c54/a7f/c54a7fae3f5d01b83d2bdb3d42700185104e05eb/5a9808f2cedaec641ac9f872e539f852c81aa7fc/FormFactorQuality.json @@ -0,0 +1 @@ +[0.0262, 77.1194] \ No newline at end of file diff --git a/Simulations/c54/a7f/c54a7fae3f5d01b83d2bdb3d42700185104e05eb/5a9808f2cedaec641ac9f872e539f852c81aa7fc/README.yaml b/Simulations/c54/a7f/c54a7fae3f5d01b83d2bdb3d42700185104e05eb/5a9808f2cedaec641ac9f872e539f852c81aa7fc/README.yaml index 3a139efba1..7b318db6a8 100644 --- a/Simulations/c54/a7f/c54a7fae3f5d01b83d2bdb3d42700185104e05eb/5a9808f2cedaec641ac9f872e539f852c81aa7fc/README.yaml +++ b/Simulations/c54/a7f/c54a7fae3f5d01b83d2bdb3d42700185104e05eb/5a9808f2cedaec641ac9f872e539f852c81aa7fc/README.yaml @@ -39,3 +39,9 @@ NUMBER_OF_ATOMS: 53000 DATEOFRUNNING: 15/09/2026 TYPEOFSYSTEM: lipid bilayer ID: 936 +EXPERIMENT: + ORDERPARAMETER: + DPPC: + - 10.1021/bi00687a021/1 + FORMFACTOR: + - 10.1016/j.bbamem.2011.07.022/4 diff --git a/Simulations/c54/a7f/c54a7fae3f5d01b83d2bdb3d42700185104e05eb/5a9808f2cedaec641ac9f872e539f852c81aa7fc/SYSTEM_quality.json b/Simulations/c54/a7f/c54a7fae3f5d01b83d2bdb3d42700185104e05eb/5a9808f2cedaec641ac9f872e539f852c81aa7fc/SYSTEM_quality.json new file mode 100644 index 0000000000..77d2a59c82 --- /dev/null +++ b/Simulations/c54/a7f/c54a7fae3f5d01b83d2bdb3d42700185104e05eb/5a9808f2cedaec641ac9f872e539f852c81aa7fc/SYSTEM_quality.json @@ -0,0 +1 @@ +{"headgroup": 0.6337, "tails": 0.0, "total": 0.6337} \ No newline at end of file diff --git a/Simulations/c5a/0fd/c5a0fdba5422ce32b4276ab2f414f589cb8ffa61/f054918c6e81100f6730817e426eb0e2f652190e/README.yaml b/Simulations/c5a/0fd/c5a0fdba5422ce32b4276ab2f414f589cb8ffa61/f054918c6e81100f6730817e426eb0e2f652190e/README.yaml index 1db103d566..e709046dc3 100644 --- a/Simulations/c5a/0fd/c5a0fdba5422ce32b4276ab2f414f589cb8ffa61/f054918c6e81100f6730817e426eb0e2f652190e/README.yaml +++ b/Simulations/c5a/0fd/c5a0fdba5422ce32b4276ab2f414f589cb8ffa61/f054918c6e81100f6730817e426eb0e2f652190e/README.yaml @@ -49,9 +49,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 308 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (80:20) bilayer at 310 K (Slipids, GROMACS 4.6, 500 ns) [NMRlipids simulation 308] + name: Molecular dynamics trajectory of a POPC/CHOL (80:20) bilayer at 310 K (Slipids, + GROMACS 4.6, 500 ns) [NMRlipids simulation 308] alternateName: 200POPC_9000SOL_50CHOL_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 80 mol%) and 50 CHOL (cholesterol, 20 mol%) at 310 K. Simulated with Slipids in GROMACS 4.6 for 500 ns (57500 atoms). Deposited as NMRlipids Databank simulation 308 and available from https://doi.org/10.5281/zenodo.3243328. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 80 mol%) and 50 CHOL (cholesterol, 20 mol%) at 310 K. Simulated with Slipids in + GROMACS 4.6 for 500 ns (57500 atoms). Deposited as NMRlipids Databank simulation + 308 and available from https://doi.org/10.5281/zenodo.3243328. sameAs: https://doi.org/10.5281/zenodo.3243328 datePublished: '2016-08-22' license: @@ -140,7 +144,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3243328 identifier: 10.5281/zenodo.3243328 url: https://doi.org/10.5281/zenodo.3243328 - name: POPC with 0, 10, 20, and 30 mol-% of cholesterol at 310 K. Slipids force field. + name: POPC with 0, 10, 20, and 30 mol-% of cholesterol at 310 K. Slipids force + field. publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/c5d/0ee/c5d0eefdf6f7a195c45bd176ff8fdcbd850cf4d1/cf6ec9d22479f5e5d0850e238d6f5d0102a21790/README.yaml b/Simulations/c5d/0ee/c5d0eefdf6f7a195c45bd176ff8fdcbd850cf4d1/cf6ec9d22479f5e5d0850e238d6f5d0102a21790/README.yaml index fd56553864..7fa2fcdbc8 100644 --- a/Simulations/c5d/0ee/c5d0eefdf6f7a195c45bd176ff8fdcbd850cf4d1/cf6ec9d22479f5e5d0850e238d6f5d0102a21790/README.yaml +++ b/Simulations/c5d/0ee/c5d0eefdf6f7a195c45bd176ff8fdcbd850cf4d1/cf6ec9d22479f5e5d0850e238d6f5d0102a21790/README.yaml @@ -55,9 +55,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 198 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (60:27:13) bilayer at 313 K (ECC-lipids, GROMACS 5.1.4, 300 ns) [NMRlipids simulation 198] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (60:27:13) bilayer at 313 + K (ECC-lipids, GROMACS 5.1.4, 300 ns) [NMRlipids simulation 198] alternateName: 128POPC_6400SOL_29CAL_58CLA_313K_OPC3model - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 60 mol%), 58 CLA (27 mol%) and 29 CAL (13 mol%) at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 300 ns (36439 atoms). Deposited as NMRlipids Databank simulation 198 and available from https://doi.org/10.5281/zenodo.1118980. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 60 mol%), 58 CLA (27 mol%) and 29 CAL (13 mol%) at 313 K. Simulated with ECC-lipids + in GROMACS 5.1.4 for 300 ns (36439 atoms). Deposited as NMRlipids Databank simulation + 198 and available from https://doi.org/10.5281/zenodo.1118980. sameAs: https://doi.org/10.5281/zenodo.1118980 datePublished: '2017-12-19' license: @@ -147,7 +151,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1118980 identifier: 10.5281/zenodo.1118980 url: https://doi.org/10.5281/zenodo.1118980 - name: Simulations Of Popc Lipid Bilayer In Water Solution At Various Nacl And Cacl2 Concentrations Using Ecc-Popc Force Field And Various Water Models + name: Simulations Of Popc Lipid Bilayer In Water Solution At Various Nacl And + Cacl2 Concentrations Using Ecc-Popc Force Field And Various Water Models publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/c67/a60/c67a6003fec136c382187dddcd9782fd9dfe17e5/c67a6003fec136c382187dddcd9782fd9dfe17e5/README.yaml b/Simulations/c67/a60/c67a6003fec136c382187dddcd9782fd9dfe17e5/c67a6003fec136c382187dddcd9782fd9dfe17e5/README.yaml index 81e97c6029..70df0bc720 100644 --- a/Simulations/c67/a60/c67a6003fec136c382187dddcd9782fd9dfe17e5/c67a6003fec136c382187dddcd9782fd9dfe17e5/README.yaml +++ b/Simulations/c67/a60/c67a6003fec136c382187dddcd9782fd9dfe17e5/c67a6003fec136c382187dddcd9782fd9dfe17e5/README.yaml @@ -43,9 +43,12 @@ EXPERIMENT: FORMFACTOR: - 10.1016/j.bbamem.2011.07.022/4 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC bilayer at 323 K (CHARMM36-LJPME, OPENMM, 300 ns) [NMRlipids simulation 728] + name: Molecular dynamics trajectory of a DPPC bilayer at 323 K (CHARMM36-LJPME, + OPENMM, 300 ns) [NMRlipids simulation 728] alternateName: DPPC_SOL_323K - description: Molecular dynamics trajectory of a lipid bilayer of 288 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) at 323 K. Simulated with CHARMM36-LJPME in OPENMM for 300 ns (64224 atoms). Deposited as NMRlipids Databank simulation 728 and available from https://doi.org/10.5281/zenodo.7476579. + description: Molecular dynamics trajectory of a lipid bilayer of 288 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) + at 323 K. Simulated with CHARMM36-LJPME in OPENMM for 300 ns (64224 atoms). Deposited + as NMRlipids Databank simulation 728 and available from https://doi.org/10.5281/zenodo.7476579. sameAs: https://doi.org/10.5281/zenodo.7476579 datePublished: '2022-02-02' license: diff --git a/Simulations/c68/041/c680410d7e6010621242fd9ae5c9d1cd0e601997/641ca89d6f2450268ecb94cd0a688fb423bc6e9b/README.yaml b/Simulations/c68/041/c680410d7e6010621242fd9ae5c9d1cd0e601997/641ca89d6f2450268ecb94cd0a688fb423bc6e9b/README.yaml index ad798039f0..311c8cf8a8 100644 --- a/Simulations/c68/041/c680410d7e6010621242fd9ae5c9d1cd0e601997/641ca89d6f2450268ecb94cd0a688fb423bc6e9b/README.yaml +++ b/Simulations/c68/041/c680410d7e6010621242fd9ae5c9d1cd0e601997/641ca89d6f2450268ecb94cd0a688fb423bc6e9b/README.yaml @@ -50,9 +50,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 130 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (48:35:17) bilayer at 370 K (Slipids with ECC-scaled ions (Kohagen), GROMACS 4.6, 800 ns) [NMRlipids simulation 130] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (48:35:17) bilayer at 370 + K (Slipids with ECC-scaled ions (Kohagen), GROMACS 4.6, 800 ns) [NMRlipids simulation + 130] alternateName: 200POPC_9000SOL_73CAL_146CLA_370K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 48 mol%), 146 CLA (35 mol%) and 73 CAL (17 mol%) at 370 K. Simulated with Slipids with ECC-scaled ions (Kohagen) in GROMACS 4.6 for 800 ns (54019 atoms). Deposited as NMRlipids Databank simulation 130 and available from https://doi.org/10.5281/zenodo.259354. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 48 mol%), 146 CLA (35 mol%) and 73 CAL (17 mol%) at 370 K. Simulated with Slipids + with ECC-scaled ions (Kohagen) in GROMACS 4.6 for 800 ns (54019 atoms). Deposited + as NMRlipids Databank simulation 130 and available from https://doi.org/10.5281/zenodo.259354. sameAs: https://doi.org/10.5281/zenodo.259354 datePublished: '2017-01-24' license: @@ -140,7 +145,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.259354 identifier: 10.5281/zenodo.259354 url: https://doi.org/10.5281/zenodo.259354 - name: Popc With Varying Amounts Of Cholesterol, 450 Mm Of Cacl_2. Slipids With Ecc-Scaled Ions + name: Popc With Varying Amounts Of Cholesterol, 450 Mm Of Cacl_2. Slipids With + Ecc-Scaled Ions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/c6a/82c/c6a82c8fe511a96186297ea337b3cea003752a62/5e952b8e3ed5724a96ce3b3c3a6515a926e2b124/README.yaml b/Simulations/c6a/82c/c6a82c8fe511a96186297ea337b3cea003752a62/5e952b8e3ed5724a96ce3b3c3a6515a926e2b124/README.yaml index 1dfc1339b4..2c1c25c2f9 100644 --- a/Simulations/c6a/82c/c6a82c8fe511a96186297ea337b3cea003752a62/5e952b8e3ed5724a96ce3b3c3a6515a926e2b124/README.yaml +++ b/Simulations/c6a/82c/c6a82c8fe511a96186297ea337b3cea003752a62/5e952b8e3ed5724a96ce3b3c3a6515a926e2b124/README.yaml @@ -50,9 +50,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/3 ID: 663 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (89:11) bilayer at 298.15 K (Lipid17, GROMACS 2021, 1001 ns) [NMRlipids simulation 663] + name: Molecular dynamics trajectory of a POPC/CHOL (89:11) bilayer at 298.15 K (Lipid17, + GROMACS 2021, 1001 ns) [NMRlipids simulation 663] alternateName: Lipid17_POPC_CHOL11_L - description: Molecular dynamics trajectory of a lipid bilayer of 1024 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 89 mol%) and 128 CHOL (cholesterol, 11 mol%) at 298.15 K. Simulated with Lipid17 in GROMACS 2021 for 1001 ns (319488 atoms). Deposited as NMRlipids Databank simulation 663 and available from https://doi.org/10.5281/zenodo.6992065. + description: Molecular dynamics trajectory of a lipid bilayer of 1024 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 89 mol%) and 128 CHOL (cholesterol, 11 mol%) at 298.15 K. Simulated with Lipid17 + in GROMACS 2021 for 1001 ns (319488 atoms). Deposited as NMRlipids Databank simulation + 663 and available from https://doi.org/10.5281/zenodo.6992065. sameAs: https://doi.org/10.5281/zenodo.6992065 datePublished: '2022-08-15' license: diff --git a/Simulations/c6f/a9f/c6fa9fb38f56ad45034039bae9ac44921559d9e3/82f1c9042c4a1b7e9d7c4c0dd889cc9aa85d9898/README.yaml b/Simulations/c6f/a9f/c6fa9fb38f56ad45034039bae9ac44921559d9e3/82f1c9042c4a1b7e9d7c4c0dd889cc9aa85d9898/README.yaml index c4a8e0ae49..3410fd220b 100644 --- a/Simulations/c6f/a9f/c6fa9fb38f56ad45034039bae9ac44921559d9e3/82f1c9042c4a1b7e9d7c4c0dd889cc9aa85d9898/README.yaml +++ b/Simulations/c6f/a9f/c6fa9fb38f56ad45034039bae9ac44921559d9e3/82f1c9042c4a1b7e9d7c4c0dd889cc9aa85d9898/README.yaml @@ -42,9 +42,13 @@ EXPERIMENT: C20: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/C20 (86:14) bilayer at 333 K (CHARMM36, GROMACS, 100 ns) [NMRlipids simulation 891] + name: Molecular dynamics trajectory of a DPPC/C20 (86:14) bilayer at 333 K (CHARMM36, + GROMACS, 100 ns) [NMRlipids simulation 891] alternateName: DPPC/C20 - description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 86 mol%) and 12 C20 (n-Eicosane, 14 mol%) at 333 K. Simulated with CHARMM36 in GROMACS for 100 ns (13977 atoms). Deposited as NMRlipids Databank simulation 891 and available from https://doi.org/10.5281/zenodo.7572990. + description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 86 mol%) and 12 C20 (n-Eicosane, 14 mol%) at 333 K. Simulated with CHARMM36 in + GROMACS for 100 ns (13977 atoms). Deposited as NMRlipids Databank simulation 891 + and available from https://doi.org/10.5281/zenodo.7572990. sameAs: https://doi.org/10.5281/zenodo.7572990 datePublished: '2023-01-26' license: @@ -137,7 +141,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.7572990 identifier: 10.5281/zenodo.7572990 url: https://doi.org/10.5281/zenodo.7572990 - name: 'MD simulation input files and results for ,,Atomistic MD simulations of n-alkanes in a phospholipid bilayer: CHARMM36 versus Slipids"' + name: 'MD simulation input files and results for ,,Atomistic MD simulations of + n-alkanes in a phospholipid bilayer: CHARMM36 versus Slipids"' publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/c70/966/c70966a89d7579487035167bda3096a9ec0ba25f/a792ffbee10c8683ef44830a943d35139d1add6d/README.yaml b/Simulations/c70/966/c70966a89d7579487035167bda3096a9ec0ba25f/a792ffbee10c8683ef44830a943d35139d1add6d/README.yaml index 399e1507a5..f0ef0e6457 100644 --- a/Simulations/c70/966/c70966a89d7579487035167bda3096a9ec0ba25f/a792ffbee10c8683ef44830a943d35139d1add6d/README.yaml +++ b/Simulations/c70/966/c70966a89d7579487035167bda3096a9ec0ba25f/a792ffbee10c8683ef44830a943d35139d1add6d/README.yaml @@ -52,9 +52,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/5 ID: 72 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (80:20) bilayer at 298.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 72] + name: Molecular dynamics trajectory of a POPC/CHOL (80:20) bilayer at 298.15 K (CHARMM36, + GROMACS, 1001 ns) [NMRlipids simulation 72] alternateName: 256POPC_64CHOL_16000SOL_298K - description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 80 mol%) and 64 CHOL (cholesterol, 20 mol%) at 298.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (87040 atoms). Deposited as NMRlipids Databank simulation 72 and available from https://doi.org/10.5281/zenodo.5767451. + description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 80 mol%) and 64 CHOL (cholesterol, 20 mol%) at 298.15 K. Simulated with CHARMM36 + in GROMACS for 1001 ns (87040 atoms). Deposited as NMRlipids Databank simulation + 72 and available from https://doi.org/10.5281/zenodo.5767451. sameAs: https://doi.org/10.5281/zenodo.5767451 datePublished: '2021-12-08' license: diff --git a/Simulations/c74/6ca/c746ca52b71d685e53a802e8046e1253baf6af2b/8850a90345eb033df4ae3228c3b9fa1fbbe40162/README.yaml b/Simulations/c74/6ca/c746ca52b71d685e53a802e8046e1253baf6af2b/8850a90345eb033df4ae3228c3b9fa1fbbe40162/README.yaml index 35aac65bbf..ffae9eb9af 100644 --- a/Simulations/c74/6ca/c746ca52b71d685e53a802e8046e1253baf6af2b/8850a90345eb033df4ae3228c3b9fa1fbbe40162/README.yaml +++ b/Simulations/c74/6ca/c746ca52b71d685e53a802e8046e1253baf6af2b/8850a90345eb033df4ae3228c3b9fa1fbbe40162/README.yaml @@ -47,9 +47,13 @@ EXPERIMENT: ID: 307 AUTHORS_CONTACT: Javanainen, Matti bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPG/SOD (33:33:33) bilayer at 298 K (Slipids, GROMACS, 500 ns) [NMRlipids simulation 307] + name: Molecular dynamics trajectory of a POPC/POPG/SOD (33:33:33) bilayer at 298 + K (Slipids, GROMACS, 500 ns) [NMRlipids simulation 307] alternateName: POPC_T298K - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 33 mol%), 128 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 33 mol%) and 128 SOD (33 mol%) at 298 K. Simulated with Slipids in GROMACS for 500 ns (71936 atoms). Deposited as NMRlipids Databank simulation 307 and available from https://doi.org/10.5281/zenodo.3613573. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 33 mol%), 128 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 33 mol%) + and 128 SOD (33 mol%) at 298 K. Simulated with Slipids in GROMACS for 500 ns (71936 + atoms). Deposited as NMRlipids Databank simulation 307 and available from https://doi.org/10.5281/zenodo.3613573. sameAs: https://doi.org/10.5281/zenodo.3613573 datePublished: '2020-01-13' license: @@ -138,7 +142,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3613573 identifier: 10.5281/zenodo.3613573 url: https://doi.org/10.5281/zenodo.3613573 - name: Simulations of POPC:POPG 1:1 membranes with varying levels of CaCl_2 using the Slipids force field + name: Simulations of POPC:POPG 1:1 membranes with varying levels of CaCl_2 using + the Slipids force field publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/c7b/d80/c7bd80cd798032ce5c45e59a8db3d833e7190373/de8cf5a17069104a442d6ed55f2d001c7f51786b/README.yaml b/Simulations/c7b/d80/c7bd80cd798032ce5c45e59a8db3d833e7190373/de8cf5a17069104a442d6ed55f2d001c7f51786b/README.yaml index ae818cda27..611cd774a5 100644 --- a/Simulations/c7b/d80/c7bd80cd798032ce5c45e59a8db3d833e7190373/de8cf5a17069104a442d6ed55f2d001c7f51786b/README.yaml +++ b/Simulations/c7b/d80/c7bd80cd798032ce5c45e59a8db3d833e7190373/de8cf5a17069104a442d6ed55f2d001c7f51786b/README.yaml @@ -50,9 +50,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 856 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (89:7:4) bilayer at 300 K (CHARMM36, GROMACS 2019.5, 100 ns) [NMRlipids simulation 856] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (89:7:4) bilayer at 300 K + (CHARMM36, GROMACS 2019.5, 100 ns) [NMRlipids simulation 856] alternateName: POPC, 44 w/l, 300 K, 0.05 M CaCl2 - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 89 mol%), 16 CLA (7 mol%) and 8 CAL (4 mol%) at 300 K. Simulated with CHARMM36 in GROMACS 2019.5 for 100 ns (53464 atoms). Deposited as NMRlipids Databank simulation 856 and available from https://doi.org/10.5281/zenodo.6341899. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 89 mol%), 16 CLA (7 mol%) and 8 CAL (4 mol%) at 300 K. Simulated with CHARMM36 + in GROMACS 2019.5 for 100 ns (53464 atoms). Deposited as NMRlipids Databank simulation + 856 and available from https://doi.org/10.5281/zenodo.6341899. sameAs: https://doi.org/10.5281/zenodo.6341899 datePublished: '2022-03-09' license: diff --git a/Simulations/c81/ebd/c81ebdad6c2c867172465d377eb97c811f698409/bc74b1c015d912a6fb2ee3176efd710e4e3534e8/README.yaml b/Simulations/c81/ebd/c81ebdad6c2c867172465d377eb97c811f698409/bc74b1c015d912a6fb2ee3176efd710e4e3534e8/README.yaml index 30e50be86a..5034b399c7 100644 --- a/Simulations/c81/ebd/c81ebdad6c2c867172465d377eb97c811f698409/bc74b1c015d912a6fb2ee3176efd710e4e3534e8/README.yaml +++ b/Simulations/c81/ebd/c81ebdad6c2c867172465d377eb97c811f698409/bc74b1c015d912a6fb2ee3176efd710e4e3534e8/README.yaml @@ -55,9 +55,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 22 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (52:32:16) bilayer at 313 K (ECC-lipids, GROMACS 5.1.4, 300 ns) [NMRlipids simulation 22] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (52:32:16) bilayer at 313 + K (ECC-lipids, GROMACS 5.1.4, 300 ns) [NMRlipids simulation 22] alternateName: 128POPC_6400SOL_40CAL_80CLA_313K - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 52 mol%), 80 CLA (32 mol%) and 40 CAL (16 mol%) at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 300 ns (36472 atoms). Deposited as NMRlipids Databank simulation 22 and available from https://doi.org/10.5281/zenodo.3335503. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 52 mol%), 80 CLA (32 mol%) and 40 CAL (16 mol%) at 313 K. Simulated with ECC-lipids + in GROMACS 5.1.4 for 300 ns (36472 atoms). Deposited as NMRlipids Databank simulation + 22 and available from https://doi.org/10.5281/zenodo.3335503. sameAs: https://doi.org/10.5281/zenodo.3335503 datePublished: '2017-12-19' license: @@ -149,7 +153,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3335503 identifier: 10.5281/zenodo.3335503 url: https://doi.org/10.5281/zenodo.3335503 - name: Simulations of POPC lipid bilayer in water solution at various NaCl, KCl and CaCl2 concentrations using ECC-POPC force field + name: Simulations of POPC lipid bilayer in water solution at various NaCl, KCl + and CaCl2 concentrations using ECC-POPC force field publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/c85/989/c859898a52a7f5008ecdaa6543f04b293ed846be/1c422966f33deaa912c3b8cc38f39115b4e0e3a4/README.yaml b/Simulations/c85/989/c859898a52a7f5008ecdaa6543f04b293ed846be/1c422966f33deaa912c3b8cc38f39115b4e0e3a4/README.yaml index dbfafc8b0f..62adf0d5dd 100644 --- a/Simulations/c85/989/c859898a52a7f5008ecdaa6543f04b293ed846be/1c422966f33deaa912c3b8cc38f39115b4e0e3a4/README.yaml +++ b/Simulations/c85/989/c859898a52a7f5008ecdaa6543f04b293ed846be/1c422966f33deaa912c3b8cc38f39115b4e0e3a4/README.yaml @@ -50,9 +50,13 @@ WARNINGS: PBC: z-jumps ID: 566 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (94:6) bilayer at 303 K (Lipid14, GROMACS 5.0.4, 200 ns) [NMRlipids simulation 566] + name: Molecular dynamics trajectory of a POPC/CHOL (94:6) bilayer at 303 K (Lipid14, + GROMACS 5.0.4, 200 ns) [NMRlipids simulation 566] alternateName: 120POPC_8CHOL_3968SOL_303K - description: Molecular dynamics trajectory of a lipid bilayer of 120 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 94 mol%) and 8 CHOL (cholesterol, 6 mol%) at 303 K. Simulated with Lipid14 in GROMACS 5.0.4 for 200 ns (28576 atoms). Deposited as NMRlipids Databank simulation 566 and available from https://doi.org/10.5281/zenodo.3870998. + description: Molecular dynamics trajectory of a lipid bilayer of 120 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 94 mol%) and 8 CHOL (cholesterol, 6 mol%) at 303 K. Simulated with Lipid14 in + GROMACS 5.0.4 for 200 ns (28576 atoms). Deposited as NMRlipids Databank simulation + 566 and available from https://doi.org/10.5281/zenodo.3870998. sameAs: https://doi.org/10.5281/zenodo.3870998 datePublished: '2020-06-01' license: @@ -141,7 +145,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3870998 identifier: 10.5281/zenodo.3870998 url: https://doi.org/10.5281/zenodo.3870998 - name: 'MD simulations of bilayers containing POPC and Cholesterol: 120POPC_8CHL_31Nwat_neutral (lipid14)' + name: 'MD simulations of bilayers containing POPC and Cholesterol: 120POPC_8CHL_31Nwat_neutral + (lipid14)' publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/c8d/480/c8d4800c75a3fdfc9204998a72df995488a5d4e5/8de6fca080f91a5028142db5a04fe0b390ad16dc/README.yaml b/Simulations/c8d/480/c8d4800c75a3fdfc9204998a72df995488a5d4e5/8de6fca080f91a5028142db5a04fe0b390ad16dc/README.yaml index 1e99ba0764..b12d6cbd8c 100644 --- a/Simulations/c8d/480/c8d4800c75a3fdfc9204998a72df995488a5d4e5/8de6fca080f91a5028142db5a04fe0b390ad16dc/README.yaml +++ b/Simulations/c8d/480/c8d4800c75a3fdfc9204998a72df995488a5d4e5/8de6fca080f91a5028142db5a04fe0b390ad16dc/README.yaml @@ -56,9 +56,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 588 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/CHOL/CLA/SOD (70:13:9:9) bilayer at 310 K (Slipids, GROMACS, 1000 ns) [NMRlipids simulation 588] + name: Molecular dynamics trajectory of a DPPC/CHOL/CLA/SOD (70:13:9:9) bilayer at + 310 K (Slipids, GROMACS, 1000 ns) [NMRlipids simulation 588] alternateName: 976DPPC_176CHOL_46440SOL_124SOD_124CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 976 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 70 mol%), 176 CHOL (cholesterol, 13 mol%), 124 CLA (9 mol%) and 124 SOD (9 mol%) at 310 K. Simulated with Slipids in GROMACS for 1000 ns (279472 atoms). Deposited as NMRlipids Databank simulation 588 and available from https://doi.org/10.5281/zenodo.3540513. + description: Molecular dynamics trajectory of a lipid bilayer of 976 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 70 mol%), 176 CHOL (cholesterol, 13 mol%), 124 CLA (9 mol%) and 124 SOD (9 mol%) + at 310 K. Simulated with Slipids in GROMACS for 1000 ns (279472 atoms). Deposited + as NMRlipids Databank simulation 588 and available from https://doi.org/10.5281/zenodo.3540513. sameAs: https://doi.org/10.5281/zenodo.3540513 datePublished: '2019-11-13' license: diff --git a/Simulations/c8d/54f/c8d54fda73085e3f9685615b4cccc6a3dffc7442/62808d96749eaff3b5572316cb0fbaa4d0863267/README.yaml b/Simulations/c8d/54f/c8d54fda73085e3f9685615b4cccc6a3dffc7442/62808d96749eaff3b5572316cb0fbaa4d0863267/README.yaml index 26010acad0..c7a0f606a4 100644 --- a/Simulations/c8d/54f/c8d54fda73085e3f9685615b4cccc6a3dffc7442/62808d96749eaff3b5572316cb0fbaa4d0863267/README.yaml +++ b/Simulations/c8d/54f/c8d54fda73085e3f9685615b4cccc6a3dffc7442/62808d96749eaff3b5572316cb0fbaa4d0863267/README.yaml @@ -56,9 +56,14 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/4 ID: 589 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (86:14) bilayer at 298 K (Berger and Modified Höltje model for cholesterol, GROMACS 4.5, 50 ns) [NMRlipids simulation 589] + name: Molecular dynamics trajectory of a POPC/CHOL (86:14) bilayer at 298 K (Berger + and Modified Höltje model for cholesterol, GROMACS 4.5, 50 ns) [NMRlipids simulation + 589] alternateName: 18CHOL_110POPC_8481SOL_298K_Berger - description: Molecular dynamics trajectory of a lipid bilayer of 110 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 86 mol%) and 18 CHOL (cholesterol, 14 mol%) at 298 K. Simulated with Berger and Modified Höltje model for cholesterol in GROMACS 4.5 for 50 ns (31685 atoms). Deposited as NMRlipids Databank simulation 589 and available from https://doi.org/10.5281/zenodo.4643914. + description: Molecular dynamics trajectory of a lipid bilayer of 110 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 86 mol%) and 18 CHOL (cholesterol, 14 mol%) at 298 K. Simulated with Berger and + Modified Höltje model for cholesterol in GROMACS 4.5 for 50 ns (31685 atoms). + Deposited as NMRlipids Databank simulation 589 and available from https://doi.org/10.5281/zenodo.4643914. sameAs: https://doi.org/10.5281/zenodo.4643914 datePublished: '2014-12-17' license: @@ -154,7 +159,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.4643914 identifier: 10.5281/zenodo.4643914 url: https://doi.org/10.5281/zenodo.4643914 - name: MD simulation trajectory and related files for POPC/cholesterol (15 mol%) bilayer (Berger model delivered by Tieleman, modified Höltje, Gromacs 4.5) + name: MD simulation trajectory and related files for POPC/cholesterol (15 mol%) + bilayer (Berger model delivered by Tieleman, modified Höltje, Gromacs 4.5) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/c9e/985/c9e985cb70acd82494121b4fbe3bda51ed74fcbb/533a5bf623d80cedabf98d97d03d5b0602b869d8/README.yaml b/Simulations/c9e/985/c9e985cb70acd82494121b4fbe3bda51ed74fcbb/533a5bf623d80cedabf98d97d03d5b0602b869d8/README.yaml index 00ec25e639..b1288701ba 100644 --- a/Simulations/c9e/985/c9e985cb70acd82494121b4fbe3bda51ed74fcbb/533a5bf623d80cedabf98d97d03d5b0602b869d8/README.yaml +++ b/Simulations/c9e/985/c9e985cb70acd82494121b4fbe3bda51ed74fcbb/533a5bf623d80cedabf98d97d03d5b0602b869d8/README.yaml @@ -50,9 +50,13 @@ SOFTWARE: gromacs DIR_WRK: /usr/home/bort/Databank ID: 256 bioschema_properties: - name: Molecular dynamics trajectory of a DAPC/CHOL (61:39) bilayer at 310 K (CHARMM36, GROMACS, 1000 ns) [NMRlipids simulation 256] + name: Molecular dynamics trajectory of a DAPC/CHOL (61:39) bilayer at 310 K (CHARMM36, + GROMACS, 1000 ns) [NMRlipids simulation 256] alternateName: 176DAPC_112CHOL_11520SOL_310K - description: Molecular dynamics trajectory of a lipid bilayer of 176 DAPC (1,2-diarachidonoyl-sn-glycero-3-phosphocholine, 61 mol%) and 112 CHOL (cholesterol, 39 mol%) at 310 K. Simulated with CHARMM36 in GROMACS for 1000 ns (67136 atoms). Deposited as NMRlipids Databank simulation 256 and available from https://doi.org/10.5281/zenodo.2653721. + description: Molecular dynamics trajectory of a lipid bilayer of 176 DAPC (1,2-diarachidonoyl-sn-glycero-3-phosphocholine, + 61 mol%) and 112 CHOL (cholesterol, 39 mol%) at 310 K. Simulated with CHARMM36 + in GROMACS for 1000 ns (67136 atoms). Deposited as NMRlipids Databank simulation + 256 and available from https://doi.org/10.5281/zenodo.2653721. sameAs: https://doi.org/10.5281/zenodo.2653721 datePublished: '2019-04-29' license: @@ -141,7 +145,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.2653721 identifier: 10.5281/zenodo.2653721 url: https://doi.org/10.5281/zenodo.2653721 - name: Atomistic simulations of cholesterol in symmetric lipid bilayers with varying degrees of lipid chain unsaturation + name: Atomistic simulations of cholesterol in symmetric lipid bilayers with varying + degrees of lipid chain unsaturation publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/ca0/8ab/ca08ab0d6dd66590d203c5094ae8fc20489670f5/7317b6b19cfb16559c47fa2feaad2a1e1d903823/README.yaml b/Simulations/ca0/8ab/ca08ab0d6dd66590d203c5094ae8fc20489670f5/7317b6b19cfb16559c47fa2feaad2a1e1d903823/README.yaml index 5b2648d064..ba8e0aaaa9 100644 --- a/Simulations/ca0/8ab/ca08ab0d6dd66590d203c5094ae8fc20489670f5/7317b6b19cfb16559c47fa2feaad2a1e1d903823/README.yaml +++ b/Simulations/ca0/8ab/ca08ab0d6dd66590d203c5094ae8fc20489670f5/7317b6b19cfb16559c47fa2feaad2a1e1d903823/README.yaml @@ -49,9 +49,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 686 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (71:29) bilayer at 298.15 K (Lipid17, GROMACS 2021, 1001 ns) [NMRlipids simulation 686] + name: Molecular dynamics trajectory of a POPC/CHOL (71:29) bilayer at 298.15 K (Lipid17, + GROMACS 2021, 1001 ns) [NMRlipids simulation 686] alternateName: Lipid17_POPC_CHOL29_S - description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 71 mol%) and 26 CHOL (cholesterol, 29 mol%) at 298.15 K. Simulated with Lipid17 in GROMACS 2021 for 1001 ns (24000 atoms). Deposited as NMRlipids Databank simulation 686 and available from https://doi.org/10.5281/zenodo.6992065. + description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 71 mol%) and 26 CHOL (cholesterol, 29 mol%) at 298.15 K. Simulated with Lipid17 + in GROMACS 2021 for 1001 ns (24000 atoms). Deposited as NMRlipids Databank simulation + 686 and available from https://doi.org/10.5281/zenodo.6992065. sameAs: https://doi.org/10.5281/zenodo.6992065 datePublished: '2022-08-15' license: diff --git a/Simulations/ca4/038/ca403878babec6f48159c1355f202089c0fd7fc0/81adbfa5c49ae97cb93b9bbe06fa673662c1a44a/README.yaml b/Simulations/ca4/038/ca403878babec6f48159c1355f202089c0fd7fc0/81adbfa5c49ae97cb93b9bbe06fa673662c1a44a/README.yaml index 38f7080ee1..1a81ea4164 100644 --- a/Simulations/ca4/038/ca403878babec6f48159c1355f202089c0fd7fc0/81adbfa5c49ae97cb93b9bbe06fa673662c1a44a/README.yaml +++ b/Simulations/ca4/038/ca403878babec6f48159c1355f202089c0fd7fc0/81adbfa5c49ae97cb93b9bbe06fa673662c1a44a/README.yaml @@ -45,9 +45,12 @@ WARNINGS: PBC: hexagonal-box ID: 29 bioschema_properties: - name: Molecular dynamics trajectory of a POPE bilayer at 310 K (Slipids, GROMACS 5.0.6, 100 ns) [NMRlipids simulation 29] + name: Molecular dynamics trajectory of a POPE bilayer at 310 K (Slipids, GROMACS + 5.0.6, 100 ns) [NMRlipids simulation 29] alternateName: 336POPE_13460SOL_310K_v1 - description: Molecular dynamics trajectory of a lipid bilayer of 336 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) at 310 K. Simulated with Slipids in GROMACS 5.0.6 for 100 ns (82380 atoms). Deposited as NMRlipids Databank simulation 29 and available from https://doi.org/10.5281/zenodo.1293813. + description: Molecular dynamics trajectory of a lipid bilayer of 336 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) + at 310 K. Simulated with Slipids in GROMACS 5.0.6 for 100 ns (82380 atoms). Deposited + as NMRlipids Databank simulation 29 and available from https://doi.org/10.5281/zenodo.1293813. sameAs: https://doi.org/10.5281/zenodo.1293813 datePublished: '2018-06-20' license: diff --git a/Simulations/ca5/901/ca5901567ec1dc59289e7db37127ee3c88ef0df7/0c5652ab9358041f2b8ce555c01f5591e9feefea/README.yaml b/Simulations/ca5/901/ca5901567ec1dc59289e7db37127ee3c88ef0df7/0c5652ab9358041f2b8ce555c01f5591e9feefea/README.yaml index c1c8c71d0d..94a73d7e3f 100644 --- a/Simulations/ca5/901/ca5901567ec1dc59289e7db37127ee3c88ef0df7/0c5652ab9358041f2b8ce555c01f5591e9feefea/README.yaml +++ b/Simulations/ca5/901/ca5901567ec1dc59289e7db37127ee3c88ef0df7/0c5652ab9358041f2b8ce555c01f5591e9feefea/README.yaml @@ -55,9 +55,15 @@ DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 470 AUTHORS_CONTACT: Ollila, O. H. Samuli; Virtanen, I. Salla bioschema_properties: - name: Molecular dynamics trajectory of a CLA/CAL/POPC/POPG/SOD (53:26:7:7:7) bilayer at 298 K (lipid17ecc, GROMACS, 400 ns) [NMRlipids simulation 470] + name: Molecular dynamics trajectory of a CLA/CAL/POPC/POPG/SOD (53:26:7:7:7) bilayer + at 298 K (lipid17ecc, GROMACS, 400 ns) [NMRlipids simulation 470] alternateName: POPC:POPG(1:1)_T298K_1000mM_CaCl - description: Molecular dynamics trajectory of a lipid bilayer of 1138 CLA (53 mol%), 569 CAL (26 mol%), 150 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 7 mol%), 150 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 7 mol%) and 150 SOD (7 mol%) at 298 K. Simulated with lipid17ecc in GROMACS for 400 ns (130602 atoms). Deposited as NMRlipids Databank simulation 470 and available from https://doi.org/10.5281/zenodo.3862036. + description: Molecular dynamics trajectory of a lipid bilayer of 1138 CLA (53 mol%), + 569 CAL (26 mol%), 150 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 7 mol%), 150 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 7 mol%) + and 150 SOD (7 mol%) at 298 K. Simulated with lipid17ecc in GROMACS for 400 ns + (130602 atoms). Deposited as NMRlipids Databank simulation 470 and available from + https://doi.org/10.5281/zenodo.3862036. sameAs: https://doi.org/10.5281/zenodo.3862036 datePublished: '2020-05-28' license: @@ -148,7 +154,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3862036 identifier: 10.5281/zenodo.3862036 url: https://doi.org/10.5281/zenodo.3862036 - name: ECC-LIPID17 POPC-POPG 50:50 MD simulation, Na+ counterions and 1000mM CaCl2, 298K + name: ECC-LIPID17 POPC-POPG 50:50 MD simulation, Na+ counterions and 1000mM CaCl2, + 298K publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/ca9/5ea/ca95eaec9e05d0b4ef1d99e1c4577f0e4cec455c/3abfac8381036ab1ab6d06199cf5cc480c1963b0/README.yaml b/Simulations/ca9/5ea/ca95eaec9e05d0b4ef1d99e1c4577f0e4cec455c/3abfac8381036ab1ab6d06199cf5cc480c1963b0/README.yaml index f1c99eadd8..4e85121392 100644 --- a/Simulations/ca9/5ea/ca95eaec9e05d0b4ef1d99e1c4577f0e4cec455c/3abfac8381036ab1ab6d06199cf5cc480c1963b0/README.yaml +++ b/Simulations/ca9/5ea/ca95eaec9e05d0b4ef1d99e1c4577f0e4cec455c/3abfac8381036ab1ab6d06199cf5cc480c1963b0/README.yaml @@ -51,9 +51,13 @@ EXPERIMENT: CHOL: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a DOPC/CHOL (80:20) bilayer at 333.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 646] + name: Molecular dynamics trajectory of a DOPC/CHOL (80:20) bilayer at 333.15 K (CHARMM36, + GROMACS, 1001 ns) [NMRlipids simulation 646] alternateName: 64DOPC_16CHOL_4000SOL_333K - description: Molecular dynamics trajectory of a lipid bilayer of 64 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, 80 mol%) and 16 CHOL (cholesterol, 20 mol%) at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (22016 atoms). Deposited as NMRlipids Databank simulation 646 and available from https://doi.org/10.5281/zenodo.6943929. + description: Molecular dynamics trajectory of a lipid bilayer of 64 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, + 80 mol%) and 16 CHOL (cholesterol, 20 mol%) at 333.15 K. Simulated with CHARMM36 + in GROMACS for 1001 ns (22016 atoms). Deposited as NMRlipids Databank simulation + 646 and available from https://doi.org/10.5281/zenodo.6943929. sameAs: https://doi.org/10.5281/zenodo.6943929 datePublished: '2022-07-30' license: diff --git a/Simulations/caa/cc0/caacc0c3fe87fb553b097498ce0388d892ccbd2a/f9c1511f0805de9f317b9d6a54d00c3663914126/README.yaml b/Simulations/caa/cc0/caacc0c3fe87fb553b097498ce0388d892ccbd2a/f9c1511f0805de9f317b9d6a54d00c3663914126/README.yaml index 5c78d24089..6a08a8eecf 100644 --- a/Simulations/caa/cc0/caacc0c3fe87fb553b097498ce0388d892ccbd2a/f9c1511f0805de9f317b9d6a54d00c3663914126/README.yaml +++ b/Simulations/caa/cc0/caacc0c3fe87fb553b097498ce0388d892ccbd2a/f9c1511f0805de9f317b9d6a54d00c3663914126/README.yaml @@ -40,9 +40,13 @@ EXPERIMENT: C30: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/C30 (95:5) bilayer at 343 K (SLIPIDS, GROMACS, 100 ns) [NMRlipids simulation 892] + name: Molecular dynamics trajectory of a DPPC/C30 (95:5) bilayer at 343 K (SLIPIDS, + GROMACS, 100 ns) [NMRlipids simulation 892] alternateName: DPPC/C30 - description: Molecular dynamics trajectory of a lipid bilayer of 288 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 95 mol%) and 16 C30 (n-Triacontane, 5 mol%) at 343 K. Simulated with SLIPIDS in GROMACS for 100 ns (51875 atoms). Deposited as NMRlipids Databank simulation 892 and available from https://doi.org/10.5281/zenodo.7572990. + description: Molecular dynamics trajectory of a lipid bilayer of 288 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 95 mol%) and 16 C30 (n-Triacontane, 5 mol%) at 343 K. Simulated with SLIPIDS in + GROMACS for 100 ns (51875 atoms). Deposited as NMRlipids Databank simulation 892 + and available from https://doi.org/10.5281/zenodo.7572990. sameAs: https://doi.org/10.5281/zenodo.7572990 datePublished: '2023-01-26' license: @@ -134,7 +138,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.7572990 identifier: 10.5281/zenodo.7572990 url: https://doi.org/10.5281/zenodo.7572990 - name: 'MD simulation input files and results for ,,Atomistic MD simulations of n-alkanes in a phospholipid bilayer: CHARMM36 versus Slipids"' + name: 'MD simulation input files and results for ,,Atomistic MD simulations of + n-alkanes in a phospholipid bilayer: CHARMM36 versus Slipids"' publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/caf/2af/caf2afb6456dca5ee01813c6383dc16e15e6df1c/1fb975ff820d1ac4fd0bbf56f851392391caa57d/README.yaml b/Simulations/caf/2af/caf2afb6456dca5ee01813c6383dc16e15e6df1c/1fb975ff820d1ac4fd0bbf56f851392391caa57d/README.yaml index 7dbf1552ec..9926be7db2 100644 --- a/Simulations/caf/2af/caf2afb6456dca5ee01813c6383dc16e15e6df1c/1fb975ff820d1ac4fd0bbf56f851392391caa57d/README.yaml +++ b/Simulations/caf/2af/caf2afb6456dca5ee01813c6383dc16e15e6df1c/1fb975ff820d1ac4fd0bbf56f851392391caa57d/README.yaml @@ -44,9 +44,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 107 bioschema_properties: - name: Molecular dynamics trajectory of a DPPG/SOD (50:50) bilayer at 298 K (Slipids, GROMACS 5.0.4, 50 ns) [NMRlipids simulation 107] + name: Molecular dynamics trajectory of a DPPG/SOD (50:50) bilayer at 298 K (Slipids, + GROMACS 5.0.4, 50 ns) [NMRlipids simulation 107] alternateName: 288DPPG_11232SOL_288SOD_298K - description: Molecular dynamics trajectory of a lipid bilayer of 288 DPPG (1,2-dipalmitoyl-sn-glycero-3-phospho-(1’-rac-glycerol), 50 mol%) and 288 SOD (50 mol%) at 298 K. Simulated with Slipids in GROMACS 5.0.4 for 50 ns (69408 atoms). Deposited as NMRlipids Databank simulation 107 and available from https://doi.org/10.5281/zenodo.546135. + description: Molecular dynamics trajectory of a lipid bilayer of 288 DPPG (1,2-dipalmitoyl-sn-glycero-3-phospho-(1’-rac-glycerol), + 50 mol%) and 288 SOD (50 mol%) at 298 K. Simulated with Slipids in GROMACS 5.0.4 + for 50 ns (69408 atoms). Deposited as NMRlipids Databank simulation 107 and available + from https://doi.org/10.5281/zenodo.546135. sameAs: https://doi.org/10.5281/zenodo.546135 datePublished: '2017-04-13' license: @@ -134,7 +138,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.546135 identifier: 10.5281/zenodo.546135 url: https://doi.org/10.5281/zenodo.546135 - name: 'Md Simulation Trajectory Of A Fully Hydrated Dppg Bilayer @298K: Slipids, Gromacs 5.0.4. 2017.' + name: 'Md Simulation Trajectory Of A Fully Hydrated Dppg Bilayer @298K: Slipids, + Gromacs 5.0.4. 2017.' publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/cb5/f2d/cb5f2d91fdc3300af6b99d65e4868f39337d61cd/e6e496f83f3d15095b4577d84d957c4acf365782/README.yaml b/Simulations/cb5/f2d/cb5f2d91fdc3300af6b99d65e4868f39337d61cd/e6e496f83f3d15095b4577d84d957c4acf365782/README.yaml index 209501bb3f..513aafae2a 100644 --- a/Simulations/cb5/f2d/cb5f2d91fdc3300af6b99d65e4868f39337d61cd/e6e496f83f3d15095b4577d84d957c4acf365782/README.yaml +++ b/Simulations/cb5/f2d/cb5f2d91fdc3300af6b99d65e4868f39337d61cd/e6e496f83f3d15095b4577d84d957c4acf365782/README.yaml @@ -48,9 +48,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 575 bioschema_properties: - name: Molecular dynamics trajectory of a DOPS/SOD (50:50) bilayer at 303 K (CHARMM36-UA, GROMACS, 100 ns) [NMRlipids simulation 575] + name: Molecular dynamics trajectory of a DOPS/SOD (50:50) bilayer at 303 K (CHARMM36-UA, + GROMACS, 100 ns) [NMRlipids simulation 575] alternateName: 128DOPS_4480SOL_128SOD_303K_v2 - description: Molecular dynamics trajectory of a lipid bilayer of 128 DOPS (1,2-dioleoyl-sn-glycero-3-phospho-L-serine, 50 mol%) and 128 SOD (50 mol%) at 303 K. Simulated with CHARMM36-UA in GROMACS for 100 ns (22400 atoms). Deposited as NMRlipids Databank simulation 575 and available from https://doi.org/10.5281/zenodo.1129456. + description: Molecular dynamics trajectory of a lipid bilayer of 128 DOPS (1,2-dioleoyl-sn-glycero-3-phospho-L-serine, + 50 mol%) and 128 SOD (50 mol%) at 303 K. Simulated with CHARMM36-UA in GROMACS + for 100 ns (22400 atoms). Deposited as NMRlipids Databank simulation 575 and available + from https://doi.org/10.5281/zenodo.1129456. sameAs: https://doi.org/10.5281/zenodo.1129456 datePublished: '2017-12-24' license: diff --git a/Simulations/cb6/a4e/cb6a4e61e0a325800f5b553ef91daad270b0e90f/1b557b5ef6228ecffecfc31c3552fa6754cb41e8/README.yaml b/Simulations/cb6/a4e/cb6a4e61e0a325800f5b553ef91daad270b0e90f/1b557b5ef6228ecffecfc31c3552fa6754cb41e8/README.yaml index 889c11f4dd..7347e8587a 100644 --- a/Simulations/cb6/a4e/cb6a4e61e0a325800f5b553ef91daad270b0e90f/1b557b5ef6228ecffecfc31c3552fa6754cb41e8/README.yaml +++ b/Simulations/cb6/a4e/cb6a4e61e0a325800f5b553ef91daad270b0e90f/1b557b5ef6228ecffecfc31c3552fa6754cb41e8/README.yaml @@ -56,9 +56,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 471 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPS/SOD (71:14:14) bilayer at 298 K (GROMOS-CKP, GROMOS NH3 charges and PME, GROMACS, 100 ns) [NMRlipids simulation 471] + name: Molecular dynamics trajectory of a POPC/POPS/SOD (71:14:14) bilayer at 298 + K (GROMOS-CKP, GROMOS NH3 charges and PME, GROMACS, 100 ns) [NMRlipids simulation + 471] alternateName: 110POPC_22POPS_4620SOL_22SOD_298K_GROMOS-CKP_v1 - description: Molecular dynamics trajectory of a lipid bilayer of 110 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 71 mol%), 22 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 14 mol%) and 22 SOD (14 mol%) at 298 K. Simulated with GROMOS-CKP, GROMOS NH3 charges and PME in GROMACS for 100 ns (20812 atoms). Deposited as NMRlipids Databank simulation 471 and available from https://doi.org/10.5281/zenodo.1283333. + description: Molecular dynamics trajectory of a lipid bilayer of 110 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 71 mol%), 22 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 14 mol%) + and 22 SOD (14 mol%) at 298 K. Simulated with GROMOS-CKP, GROMOS NH3 charges and + PME in GROMACS for 100 ns (20812 atoms). Deposited as NMRlipids Databank simulation + 471 and available from https://doi.org/10.5281/zenodo.1283333. sameAs: https://doi.org/10.5281/zenodo.1283333 datePublished: '2018-06-05' license: @@ -147,7 +153,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1283333 identifier: 10.5281/zenodo.1283333 url: https://doi.org/10.5281/zenodo.1283333 - name: Gromos-Ckp Pops/Popc Simulations (Versions 1 And 2) 298 K With Gromos Nh3 Charges And Pme + name: Gromos-Ckp Pops/Popc Simulations (Versions 1 And 2) 298 K With Gromos Nh3 + Charges And Pme publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/cb9/dad/cb9dad3050719328c5a8e75096dd072d5e95cd11/34819948036ac704abbdcbee766296da3ecb716f/README.yaml b/Simulations/cb9/dad/cb9dad3050719328c5a8e75096dd072d5e95cd11/34819948036ac704abbdcbee766296da3ecb716f/README.yaml index 86ffc657cf..d8b7011ea1 100644 --- a/Simulations/cb9/dad/cb9dad3050719328c5a8e75096dd072d5e95cd11/34819948036ac704abbdcbee766296da3ecb716f/README.yaml +++ b/Simulations/cb9/dad/cb9dad3050719328c5a8e75096dd072d5e95cd11/34819948036ac704abbdcbee766296da3ecb716f/README.yaml @@ -44,9 +44,12 @@ EXPERIMENT: DYPC: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a DYPC bilayer at 333.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 632] + name: Molecular dynamics trajectory of a DYPC bilayer at 333.15 K (CHARMM36, GROMACS, + 1001 ns) [NMRlipids simulation 632] alternateName: 64DYPC_3200SOL_333K - description: Molecular dynamics trajectory of a lipid bilayer of 64 DYPC (1,2-(16:1$^\Delta9$)-sn-glycero-3-phosphocholine) at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (17664 atoms). Deposited as NMRlipids Databank simulation 632 and available from https://doi.org/10.5281/zenodo.6943413. + description: Molecular dynamics trajectory of a lipid bilayer of 64 DYPC (1,2-(16:1$^\Delta9$)-sn-glycero-3-phosphocholine) + at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (17664 atoms). Deposited + as NMRlipids Databank simulation 632 and available from https://doi.org/10.5281/zenodo.6943413. sameAs: https://doi.org/10.5281/zenodo.6943413 datePublished: '2022-07-30' license: @@ -134,7 +137,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.6943413 identifier: 10.5281/zenodo.6943413 url: https://doi.org/10.5281/zenodo.6943413 - name: Simulations of different single-component bilayers, three different system sizes + name: Simulations of different single-component bilayers, three different system + sizes publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/cbc/9f8/cbc9f8ea822baa6664eeaa0bb6842bbc8926848c/288fcffa692f18289a78f323ef6f57e1c22fccdd/README.yaml b/Simulations/cbc/9f8/cbc9f8ea822baa6664eeaa0bb6842bbc8926848c/288fcffa692f18289a78f323ef6f57e1c22fccdd/README.yaml index 43102e5cc2..ec2c30219b 100644 --- a/Simulations/cbc/9f8/cbc9f8ea822baa6664eeaa0bb6842bbc8926848c/288fcffa692f18289a78f323ef6f57e1c22fccdd/README.yaml +++ b/Simulations/cbc/9f8/cbc9f8ea822baa6664eeaa0bb6842bbc8926848c/288fcffa692f18289a78f323ef6f57e1c22fccdd/README.yaml @@ -50,9 +50,13 @@ SOFTWARE: gromacs DIR_WRK: /usr/home/bort/Databank ID: 549 bioschema_properties: - name: Molecular dynamics trajectory of a DAPC/CHOL (90:10) bilayer at 320 K (CHARMM36, GROMACS, 1000 ns) [NMRlipids simulation 549] + name: Molecular dynamics trajectory of a DAPC/CHOL (90:10) bilayer at 320 K (CHARMM36, + GROMACS, 1000 ns) [NMRlipids simulation 549] alternateName: 260DAPC_28CHOL_11520SOL_320K - description: Molecular dynamics trajectory of a lipid bilayer of 260 DAPC (1,2-diarachidonoyl-sn-glycero-3-phosphocholine, 90 mol%) and 28 CHOL (cholesterol, 10 mol%) at 320 K. Simulated with CHARMM36 in GROMACS for 1000 ns (72512 atoms). Deposited as NMRlipids Databank simulation 549 and available from https://doi.org/10.5281/zenodo.2653721. + description: Molecular dynamics trajectory of a lipid bilayer of 260 DAPC (1,2-diarachidonoyl-sn-glycero-3-phosphocholine, + 90 mol%) and 28 CHOL (cholesterol, 10 mol%) at 320 K. Simulated with CHARMM36 + in GROMACS for 1000 ns (72512 atoms). Deposited as NMRlipids Databank simulation + 549 and available from https://doi.org/10.5281/zenodo.2653721. sameAs: https://doi.org/10.5281/zenodo.2653721 datePublished: '2019-04-29' license: @@ -141,7 +145,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.2653721 identifier: 10.5281/zenodo.2653721 url: https://doi.org/10.5281/zenodo.2653721 - name: Atomistic simulations of cholesterol in symmetric lipid bilayers with varying degrees of lipid chain unsaturation + name: Atomistic simulations of cholesterol in symmetric lipid bilayers with varying + degrees of lipid chain unsaturation publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/cc2/166/cc2166100b478ef54929b78c9eb609a7b11adfb2/f8041785e95effea2f21de87052a08e6661af722/README.yaml b/Simulations/cc2/166/cc2166100b478ef54929b78c9eb609a7b11adfb2/f8041785e95effea2f21de87052a08e6661af722/README.yaml index d67b591493..a4bbb0c70a 100644 --- a/Simulations/cc2/166/cc2166100b478ef54929b78c9eb609a7b11adfb2/f8041785e95effea2f21de87052a08e6661af722/README.yaml +++ b/Simulations/cc2/166/cc2166100b478ef54929b78c9eb609a7b11adfb2/f8041785e95effea2f21de87052a08e6661af722/README.yaml @@ -48,9 +48,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 232 bioschema_properties: - name: Molecular dynamics trajectory of a DOPS/SOD (50:50) bilayer at 303 K (GROMOS-CKP, Berger/Chiu NH3 charges and PME, GROMACS, 100 ns) [NMRlipids simulation 232] + name: Molecular dynamics trajectory of a DOPS/SOD (50:50) bilayer at 303 K (GROMOS-CKP, + Berger/Chiu NH3 charges and PME, GROMACS, 100 ns) [NMRlipids simulation 232] alternateName: 128DOPS_4480SOL_128SOD_303K_GROMOS-CKP_v1 - description: Molecular dynamics trajectory of a lipid bilayer of 128 DOPS (1,2-dioleoyl-sn-glycero-3-phospho-L-serine, 50 mol%) and 128 SOD (50 mol%) at 303 K. Simulated with GROMOS-CKP, Berger/Chiu NH3 charges and PME in GROMACS for 100 ns (20864 atoms). Deposited as NMRlipids Databank simulation 232 and available from https://doi.org/10.5281/zenodo.1129429. + description: Molecular dynamics trajectory of a lipid bilayer of 128 DOPS (1,2-dioleoyl-sn-glycero-3-phospho-L-serine, + 50 mol%) and 128 SOD (50 mol%) at 303 K. Simulated with GROMOS-CKP, Berger/Chiu + NH3 charges and PME in GROMACS for 100 ns (20864 atoms). Deposited as NMRlipids + Databank simulation 232 and available from https://doi.org/10.5281/zenodo.1129429. sameAs: https://doi.org/10.5281/zenodo.1129429 datePublished: '2017-12-24' license: @@ -139,7 +143,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1129429 identifier: 10.5281/zenodo.1129429 url: https://doi.org/10.5281/zenodo.1129429 - name: Gromos-Ckp Dops Simulations (Versions 1 And 2) 303 K With Berger/Chiu Nh3 Charges And Pme + name: Gromos-Ckp Dops Simulations (Versions 1 And 2) 303 K With Berger/Chiu Nh3 + Charges And Pme publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/cc4/a40/cc4a403b0e807a109f793c4acf8d4893f5db01bc/6ec5d72af3c2ccb3d149982aa549b9647c8c7a8e/README.yaml b/Simulations/cc4/a40/cc4a403b0e807a109f793c4acf8d4893f5db01bc/6ec5d72af3c2ccb3d149982aa549b9647c8c7a8e/README.yaml index fa52f7e64b..43fa3df5b9 100644 --- a/Simulations/cc4/a40/cc4a403b0e807a109f793c4acf8d4893f5db01bc/6ec5d72af3c2ccb3d149982aa549b9647c8c7a8e/README.yaml +++ b/Simulations/cc4/a40/cc4a403b0e807a109f793c4acf8d4893f5db01bc/6ec5d72af3c2ccb3d149982aa549b9647c8c7a8e/README.yaml @@ -40,9 +40,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 475 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 310 K (Slipids, GROMACS 4.6, 150 ns) [NMRlipids simulation 475] + name: Molecular dynamics trajectory of a POPC bilayer at 310 K (Slipids, GROMACS + 4.6, 150 ns) [NMRlipids simulation 475] alternateName: 128POPC_5120SOL_310K - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 310 K. Simulated with Slipids in GROMACS 4.6 for 150 ns (32512 atoms). Deposited as NMRlipids Databank simulation 475 and available from https://doi.org/10.5281/zenodo.13887. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 310 K. Simulated with Slipids in GROMACS 4.6 for 150 ns (32512 atoms). Deposited + as NMRlipids Databank simulation 475 and available from https://doi.org/10.5281/zenodo.13887. sameAs: https://doi.org/10.5281/zenodo.13887 datePublished: '2015-01-12' license: diff --git a/Simulations/cca/1ef/cca1ef6b9eaa5c0d57028bd6f71119808fb34945/27ec2ac2b2c4d2791751d2139ea5f84871a295e2/README.yaml b/Simulations/cca/1ef/cca1ef6b9eaa5c0d57028bd6f71119808fb34945/27ec2ac2b2c4d2791751d2139ea5f84871a295e2/README.yaml index 042e417047..a012d335a0 100644 --- a/Simulations/cca/1ef/cca1ef6b9eaa5c0d57028bd6f71119808fb34945/27ec2ac2b2c4d2791751d2139ea5f84871a295e2/README.yaml +++ b/Simulations/cca/1ef/cca1ef6b9eaa5c0d57028bd6f71119808fb34945/27ec2ac2b2c4d2791751d2139ea5f84871a295e2/README.yaml @@ -46,9 +46,12 @@ EXPERIMENT: - 10.1529/biophysj.108.132662/1 ID: 47 bioschema_properties: - name: Molecular dynamics trajectory of a DOPC bilayer at 303.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 47] + name: Molecular dynamics trajectory of a DOPC bilayer at 303.15 K (CHARMM36, GROMACS, + 1001 ns) [NMRlipids simulation 47] alternateName: 1024DOPC_51200SOL_303K - description: Molecular dynamics trajectory of a lipid bilayer of 1024 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) at 303.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (294912 atoms). Deposited as NMRlipids Databank simulation 47 and available from https://doi.org/10.5281/zenodo.6943086. + description: Molecular dynamics trajectory of a lipid bilayer of 1024 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) + at 303.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (294912 atoms). Deposited + as NMRlipids Databank simulation 47 and available from https://doi.org/10.5281/zenodo.6943086. sameAs: https://doi.org/10.5281/zenodo.6943086 datePublished: '2022-07-30' license: diff --git a/Simulations/cce/ed9/cceed9acd871b1a3317691707306635aed22967c/dcbd604fd2397a544b77edfc2f261446f03768c1/README.yaml b/Simulations/cce/ed9/cceed9acd871b1a3317691707306635aed22967c/dcbd604fd2397a544b77edfc2f261446f03768c1/README.yaml index bb41b32d3a..16bf7a2cd2 100644 --- a/Simulations/cce/ed9/cceed9acd871b1a3317691707306635aed22967c/dcbd604fd2397a544b77edfc2f261446f03768c1/README.yaml +++ b/Simulations/cce/ed9/cceed9acd871b1a3317691707306635aed22967c/dcbd604fd2397a544b77edfc2f261446f03768c1/README.yaml @@ -50,9 +50,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 4 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/CLA/SOD (82:9:9) bilayer at 338 K (CHARMM36, GROMACS 5.0.4, 500 ns) [NMRlipids simulation 4] + name: Molecular dynamics trajectory of a DPPC/CLA/SOD (82:9:9) bilayer at 338 K + (CHARMM36, GROMACS 5.0.4, 500 ns) [NMRlipids simulation 4] alternateName: DPPC_512_NaCl_150mM_338K - description: Molecular dynamics trajectory of a lipid bilayer of 512 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 82 mol%), 55 CLA (9 mol%) and 55 SOD (9 mol%) at 338 K. Simulated with CHARMM36 in GROMACS 5.0.4 for 500 ns (128110 atoms). Deposited as NMRlipids Databank simulation 4 and available from https://doi.org/10.5281/zenodo.1009027. + description: Molecular dynamics trajectory of a lipid bilayer of 512 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 82 mol%), 55 CLA (9 mol%) and 55 SOD (9 mol%) at 338 K. Simulated with CHARMM36 + in GROMACS 5.0.4 for 500 ns (128110 atoms). Deposited as NMRlipids Databank simulation + 4 and available from https://doi.org/10.5281/zenodo.1009027. sameAs: https://doi.org/10.5281/zenodo.1009027 datePublished: '2017-10-11' license: diff --git a/Simulations/cd2/f4d/cd2f4d8af318b9109ceb1fd8befa7a3a4ac582c9/fc0718c08ed9618350691ba27d3fcece002fc31c/README.yaml b/Simulations/cd2/f4d/cd2f4d8af318b9109ceb1fd8befa7a3a4ac582c9/fc0718c08ed9618350691ba27d3fcece002fc31c/README.yaml index fc273b952a..f7c81e4d40 100644 --- a/Simulations/cd2/f4d/cd2f4d8af318b9109ceb1fd8befa7a3a4ac582c9/fc0718c08ed9618350691ba27d3fcece002fc31c/README.yaml +++ b/Simulations/cd2/f4d/cd2f4d8af318b9109ceb1fd8befa7a3a4ac582c9/fc0718c08ed9618350691ba27d3fcece002fc31c/README.yaml @@ -55,9 +55,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 571 bioschema_properties: - name: Molecular dynamics trajectory of a CLA/POPC/CAL (48:28:24) bilayer at 313 K (ECC-lipids, GROMACS 5.1.4, 300 ns) [NMRlipids simulation 571] + name: Molecular dynamics trajectory of a CLA/POPC/CAL (48:28:24) bilayer at 313 + K (ECC-lipids, GROMACS 5.1.4, 300 ns) [NMRlipids simulation 571] alternateName: 128POPC_6232SOL_110CAL_220CLA_313K_OPC3model - description: Molecular dynamics trajectory of a lipid bilayer of 220 CLA (48 mol%), 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 28 mol%) and 110 CAL (24 mol%) at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 300 ns (36178 atoms). Deposited as NMRlipids Databank simulation 571 and available from https://doi.org/10.5281/zenodo.1118980. + description: Molecular dynamics trajectory of a lipid bilayer of 220 CLA (48 mol%), + 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 28 mol%) and 110 CAL + (24 mol%) at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 300 ns (36178 + atoms). Deposited as NMRlipids Databank simulation 571 and available from https://doi.org/10.5281/zenodo.1118980. sameAs: https://doi.org/10.5281/zenodo.1118980 datePublished: '2017-12-19' license: @@ -147,7 +151,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1118980 identifier: 10.5281/zenodo.1118980 url: https://doi.org/10.5281/zenodo.1118980 - name: Simulations Of Popc Lipid Bilayer In Water Solution At Various Nacl And Cacl2 Concentrations Using Ecc-Popc Force Field And Various Water Models + name: Simulations Of Popc Lipid Bilayer In Water Solution At Various Nacl And + Cacl2 Concentrations Using Ecc-Popc Force Field And Various Water Models publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/cd5/97b/cd597b048d3bce8f2deced60b1a5c1931f58e0c3/2ff3ec74da7e2bfff2cb843dcc23246fc4e883df/README.yaml b/Simulations/cd5/97b/cd597b048d3bce8f2deced60b1a5c1931f58e0c3/2ff3ec74da7e2bfff2cb843dcc23246fc4e883df/README.yaml index e157c3ee9a..0d4f2e2ca0 100644 --- a/Simulations/cd5/97b/cd597b048d3bce8f2deced60b1a5c1931f58e0c3/2ff3ec74da7e2bfff2cb843dcc23246fc4e883df/README.yaml +++ b/Simulations/cd5/97b/cd597b048d3bce8f2deced60b1a5c1931f58e0c3/2ff3ec74da7e2bfff2cb843dcc23246fc4e883df/README.yaml @@ -51,9 +51,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 235 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (39:31:31) bilayer at 310.15 K (CHARMM36 noNBFIX, GROMACS, 863 ns) [NMRlipids simulation 235] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (39:31:31) bilayer at 310.15 + K (CHARMM36 noNBFIX, GROMACS, 863 ns) [NMRlipids simulation 235] alternateName: 200POPC_9000SOL_157SOD_157CLA_310K_noNBFIX - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 39 mol%), 157 CLA (31 mol%) and 157 SOD (31 mol%) at 310.15 K. Simulated with CHARMM36 noNBFIX in GROMACS for 863 ns (54114 atoms). Deposited as NMRlipids Databank simulation 235 and available from https://doi.org/10.5281/zenodo.3434396. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 39 mol%), 157 CLA (31 mol%) and 157 SOD (31 mol%) at 310.15 K. Simulated with + CHARMM36 noNBFIX in GROMACS for 863 ns (54114 atoms). Deposited as NMRlipids Databank + simulation 235 and available from https://doi.org/10.5281/zenodo.3434396. sameAs: https://doi.org/10.5281/zenodo.3434396 datePublished: '2019-09-17' license: diff --git a/Simulations/cd6/0b2/cd60b28028d5ff4eeb7791277dcaca5338ca8550/e0e0ecae00dc02cd003ef7b64930700db4a9a807/README.yaml b/Simulations/cd6/0b2/cd60b28028d5ff4eeb7791277dcaca5338ca8550/e0e0ecae00dc02cd003ef7b64930700db4a9a807/README.yaml index eb5d0dc1e2..22a22ba34b 100644 --- a/Simulations/cd6/0b2/cd60b28028d5ff4eeb7791277dcaca5338ca8550/e0e0ecae00dc02cd003ef7b64930700db4a9a807/README.yaml +++ b/Simulations/cd6/0b2/cd60b28028d5ff4eeb7791277dcaca5338ca8550/e0e0ecae00dc02cd003ef7b64930700db4a9a807/README.yaml @@ -55,9 +55,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 374 bioschema_properties: - name: Molecular dynamics trajectory of a CLA/POPC/CAL (48:28:24) bilayer at 313 K (ECC-lipids, GROMACS 5.1.4, 134 ns) [NMRlipids simulation 374] + name: Molecular dynamics trajectory of a CLA/POPC/CAL (48:28:24) bilayer at 313 + K (ECC-lipids, GROMACS 5.1.4, 134 ns) [NMRlipids simulation 374] alternateName: 128POPC_6232SOL_110CAL_220CLA_313K_TIP3p-FBmodel - description: Molecular dynamics trajectory of a lipid bilayer of 220 CLA (48 mol%), 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 28 mol%) and 110 CAL (24 mol%) at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 134 ns (36178 atoms). Deposited as NMRlipids Databank simulation 374 and available from https://doi.org/10.5281/zenodo.1118980. + description: Molecular dynamics trajectory of a lipid bilayer of 220 CLA (48 mol%), + 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 28 mol%) and 110 CAL + (24 mol%) at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 134 ns (36178 + atoms). Deposited as NMRlipids Databank simulation 374 and available from https://doi.org/10.5281/zenodo.1118980. sameAs: https://doi.org/10.5281/zenodo.1118980 datePublished: '2017-12-19' license: @@ -147,7 +151,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1118980 identifier: 10.5281/zenodo.1118980 url: https://doi.org/10.5281/zenodo.1118980 - name: Simulations Of Popc Lipid Bilayer In Water Solution At Various Nacl And Cacl2 Concentrations Using Ecc-Popc Force Field And Various Water Models + name: Simulations Of Popc Lipid Bilayer In Water Solution At Various Nacl And + Cacl2 Concentrations Using Ecc-Popc Force Field And Various Water Models publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/cd7/7ee/cd77eec9b016a1d67b9b618a01aad1e9b6fd0ff8/d9694447765a4eee0db2e36364db29c6aa8d3230/README.yaml b/Simulations/cd7/7ee/cd77eec9b016a1d67b9b618a01aad1e9b6fd0ff8/d9694447765a4eee0db2e36364db29c6aa8d3230/README.yaml index 03ef016d67..d21cd6ade0 100644 --- a/Simulations/cd7/7ee/cd77eec9b016a1d67b9b618a01aad1e9b6fd0ff8/d9694447765a4eee0db2e36364db29c6aa8d3230/README.yaml +++ b/Simulations/cd7/7ee/cd77eec9b016a1d67b9b618a01aad1e9b6fd0ff8/d9694447765a4eee0db2e36364db29c6aa8d3230/README.yaml @@ -56,9 +56,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 89 bioschema_properties: - name: Molecular dynamics trajectory of a SOD/POPG/POPE/CLA (44:38:13:5) bilayer at 310 K (Lipid17, GROMACS 2018.3, 92 ns) [NMRlipids simulation 89] + name: Molecular dynamics trajectory of a SOD/POPG/POPE/CLA (44:38:13:5) bilayer + at 310 K (Lipid17, GROMACS 2018.3, 92 ns) [NMRlipids simulation 89] alternateName: POPG_POPE_25000SOL_423SOD_49CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 423 SOD (44 mol%), 374 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 38 mol%), 126 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 13 mol%) and 49 CLA (5 mol%) at 310 K. Simulated with Lipid17 in GROMACS 2018.3 for 92 ns (138720 atoms). Deposited as NMRlipids Databank simulation 89 and available from https://doi.org/10.5281/zenodo.2579344. + description: Molecular dynamics trajectory of a lipid bilayer of 423 SOD (44 mol%), + 374 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 38 mol%), 126 POPE + (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 13 mol%) and 49 CLA (5 + mol%) at 310 K. Simulated with Lipid17 in GROMACS 2018.3 for 92 ns (138720 atoms). + Deposited as NMRlipids Databank simulation 89 and available from https://doi.org/10.5281/zenodo.2579344. sameAs: https://doi.org/10.5281/zenodo.2579344 datePublished: '2019-02-27' license: @@ -151,7 +156,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.2579344 identifier: 10.5281/zenodo.2579344 url: https://doi.org/10.5281/zenodo.2579344 - name: LIPID17 POPG-POPE 3:1 Bilayer Simulation (Last 100 ns, 150 mM NaCl, 310 K ) + name: LIPID17 POPG-POPE 3:1 Bilayer Simulation (Last 100 ns, 150 mM NaCl, 310 + K ) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/cda/5ce/cda5ce14c4374dd6a18f5f93ebcb02fb7893afdc/42632e1a93546847371b47eafbf6d0742a4aa445/README.yaml b/Simulations/cda/5ce/cda5ce14c4374dd6a18f5f93ebcb02fb7893afdc/42632e1a93546847371b47eafbf6d0742a4aa445/README.yaml index 3226709152..8cdecbd42f 100644 --- a/Simulations/cda/5ce/cda5ce14c4374dd6a18f5f93ebcb02fb7893afdc/42632e1a93546847371b47eafbf6d0742a4aa445/README.yaml +++ b/Simulations/cda/5ce/cda5ce14c4374dd6a18f5f93ebcb02fb7893afdc/42632e1a93546847371b47eafbf6d0742a4aa445/README.yaml @@ -64,9 +64,16 @@ EXPERIMENT: FORMFACTOR: [] ID: 491 bioschema_properties: - name: Molecular dynamics trajectory of a CLA/SOD/DPPC/DOPC/CHOL (30:30:20:16:5) bilayer at 310 K (Slipids for lipids and Smith & Dang for ions, GROMACS 4.6, 200 ns) [NMRlipids simulation 491] + name: Molecular dynamics trajectory of a CLA/SOD/DPPC/DOPC/CHOL (30:30:20:16:5) + bilayer at 310 K (Slipids for lipids and Smith & Dang for ions, GROMACS 4.6, 200 + ns) [NMRlipids simulation 491] alternateName: 204DPPC_52CHOL_166DOPC_16880SOL_304SOD_304CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 304 CLA (30 mol%), 304 SOD (30 mol%), 204 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 20 mol%), 166 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, 16 mol%) and 52 CHOL (cholesterol, 5 mol%) at 310 K. Simulated with Slipids for lipids and Smith & Dang for ions in GROMACS 4.6 for 200 ns (104524 atoms). Deposited as NMRlipids Databank simulation 491 and available from https://doi.org/10.5281/zenodo.259443. + description: Molecular dynamics trajectory of a lipid bilayer of 304 CLA (30 mol%), + 304 SOD (30 mol%), 204 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 20 mol%), + 166 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, 16 mol%) and 52 CHOL (cholesterol, + 5 mol%) at 310 K. Simulated with Slipids for lipids and Smith & Dang for ions + in GROMACS 4.6 for 200 ns (104524 atoms). Deposited as NMRlipids Databank simulation + 491 and available from https://doi.org/10.5281/zenodo.259443. sameAs: https://doi.org/10.5281/zenodo.259443 datePublished: '2017-01-24' license: diff --git a/Simulations/ce4/7a9/ce47a92a012501139c33ff522fb10f436dc57e46/4b88798894afb8a908a8688b5540cb58b0d64bda/README.yaml b/Simulations/ce4/7a9/ce47a92a012501139c33ff522fb10f436dc57e46/4b88798894afb8a908a8688b5540cb58b0d64bda/README.yaml index a4fafc6454..3922fcb106 100644 --- a/Simulations/ce4/7a9/ce47a92a012501139c33ff522fb10f436dc57e46/4b88798894afb8a908a8688b5540cb58b0d64bda/README.yaml +++ b/Simulations/ce4/7a9/ce47a92a012501139c33ff522fb10f436dc57e46/4b88798894afb8a908a8688b5540cb58b0d64bda/README.yaml @@ -42,9 +42,12 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 539 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 310.15 K (CHARMM36, GROMACS 5.0, 100 ns) [NMRlipids simulation 539] + name: Molecular dynamics trajectory of a POPC bilayer at 310.15 K (CHARMM36, GROMACS + 5.0, 100 ns) [NMRlipids simulation 539] alternateName: 1800POPC_81000SOL - description: Molecular dynamics trajectory of a lipid bilayer of 1800 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 310.15 K. Simulated with CHARMM36 in GROMACS 5.0 for 100 ns (484200 atoms). Deposited as NMRlipids Databank simulation 539 and available from https://doi.org/10.5281/zenodo.545941. + description: Molecular dynamics trajectory of a lipid bilayer of 1800 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 310.15 K. Simulated with CHARMM36 in GROMACS 5.0 for 100 ns (484200 atoms). + Deposited as NMRlipids Databank simulation 539 and available from https://doi.org/10.5281/zenodo.545941. sameAs: https://doi.org/10.5281/zenodo.545941 datePublished: '2017-04-13' license: diff --git a/Simulations/ce5/80e/ce580ea7b4e991122666ed4fc3c779e3783cbc95/e2c64d1a46b3571951cce2c90ab7302a8f300a9b/README.yaml b/Simulations/ce5/80e/ce580ea7b4e991122666ed4fc3c779e3783cbc95/e2c64d1a46b3571951cce2c90ab7302a8f300a9b/README.yaml index 369ed27151..7d0bc4020f 100644 --- a/Simulations/ce5/80e/ce580ea7b4e991122666ed4fc3c779e3783cbc95/e2c64d1a46b3571951cce2c90ab7302a8f300a9b/README.yaml +++ b/Simulations/ce5/80e/ce580ea7b4e991122666ed4fc3c779e3783cbc95/e2c64d1a46b3571951cce2c90ab7302a8f300a9b/README.yaml @@ -49,9 +49,13 @@ SOFTWARE: gromacs DIR_WRK: /usr/home/bort/Databank ID: 529 bioschema_properties: - name: Molecular dynamics trajectory of a POPS/SOD (50:50) bilayer at 298 K (Slipids, GROMACS, 100 ns) [NMRlipids simulation 529] + name: Molecular dynamics trajectory of a POPS/SOD (50:50) bilayer at 298 K (Slipids, + GROMACS, 100 ns) [NMRlipids simulation 529] alternateName: 128POPS_4880SOL_128SOD_298K_v1 - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 50 mol%) and 128 SOD (50 mol%) at 298 K. Simulated with Slipids in GROMACS for 100 ns (29824 atoms). Deposited as NMRlipids Databank simulation 529 and available from https://doi.org/10.5281/zenodo.1129441. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, + 50 mol%) and 128 SOD (50 mol%) at 298 K. Simulated with Slipids in GROMACS for + 100 ns (29824 atoms). Deposited as NMRlipids Databank simulation 529 and available + from https://doi.org/10.5281/zenodo.1129441. sameAs: https://doi.org/10.5281/zenodo.1129441 datePublished: '2017-12-24' license: diff --git a/Simulations/ce7/224/ce72249ff227687a3a83f82cde8c3aeaf0da0b9e/ce72249ff227687a3a83f82cde8c3aeaf0da0b9e/README.yaml b/Simulations/ce7/224/ce72249ff227687a3a83f82cde8c3aeaf0da0b9e/ce72249ff227687a3a83f82cde8c3aeaf0da0b9e/README.yaml index 5f949a7ee7..7cfcca4395 100644 --- a/Simulations/ce7/224/ce72249ff227687a3a83f82cde8c3aeaf0da0b9e/ce72249ff227687a3a83f82cde8c3aeaf0da0b9e/README.yaml +++ b/Simulations/ce7/224/ce72249ff227687a3a83f82cde8c3aeaf0da0b9e/ce72249ff227687a3a83f82cde8c3aeaf0da0b9e/README.yaml @@ -40,9 +40,12 @@ EXPERIMENT: - 10.1529/biophysj.108.132662/1 ID: 742 bioschema_properties: - name: Molecular dynamics trajectory of a DOPC bilayer at 303 K (AMOEBA, OPENMM v7.5.1, 202 ns) [NMRlipids simulation 742] + name: Molecular dynamics trajectory of a DOPC bilayer at 303 K (AMOEBA, OPENMM v7.5.1, + 202 ns) [NMRlipids simulation 742] alternateName: DOPC_nosalt_at_303K_with_AMOEBA - description: Molecular dynamics trajectory of a lipid bilayer of 72 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) at 303 K. Simulated with AMOEBA in OPENMM v7.5.1 for 202 ns (18576 atoms). Deposited as NMRlipids Databank simulation 742 and available from https://doi.org/10.5281/zenodo.7604681. + description: Molecular dynamics trajectory of a lipid bilayer of 72 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) + at 303 K. Simulated with AMOEBA in OPENMM v7.5.1 for 202 ns (18576 atoms). Deposited + as NMRlipids Databank simulation 742 and available from https://doi.org/10.5281/zenodo.7604681. sameAs: https://doi.org/10.5281/zenodo.7604681 datePublished: '2022-12-09' license: @@ -131,7 +134,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.7604681 identifier: 10.5281/zenodo.7604681 url: https://doi.org/10.5281/zenodo.7604681 - name: MD Simulation data for a pure DOPC bilayer without salt with AMOEBA force field + OpenMM + name: MD Simulation data for a pure DOPC bilayer without salt with AMOEBA force + field + OpenMM publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/ce8/76e/ce876e53c0e2f6f5fc73560b2bf1e8f43ea19817/cccb92e36638232a12c0d507f71f1ed737213a94/README.yaml b/Simulations/ce8/76e/ce876e53c0e2f6f5fc73560b2bf1e8f43ea19817/cccb92e36638232a12c0d507f71f1ed737213a94/README.yaml index f04f75705b..7ffff70bec 100644 --- a/Simulations/ce8/76e/ce876e53c0e2f6f5fc73560b2bf1e8f43ea19817/cccb92e36638232a12c0d507f71f1ed737213a94/README.yaml +++ b/Simulations/ce8/76e/ce876e53c0e2f6f5fc73560b2bf1e8f43ea19817/cccb92e36638232a12c0d507f71f1ed737213a94/README.yaml @@ -41,9 +41,12 @@ EXPERIMENT: FORMFACTOR: - 10.1016/j.bbamem.2011.07.022/18 bioschema_properties: - name: Molecular dynamics trajectory of a DMPC bilayer at 303.15 K (CHARMM36, GROMACS 2026.1, 100 ns) [NMRlipids simulation 910] + name: Molecular dynamics trajectory of a DMPC bilayer at 303.15 K (CHARMM36, GROMACS + 2026.1, 100 ns) [NMRlipids simulation 910] alternateName: DMPC - description: Molecular dynamics trajectory of a lipid bilayer of 40 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) at 303.15 K. Simulated with CHARMM36 in GROMACS 2026.1 for 100 ns (8800 atoms). Deposited as NMRlipids Databank simulation 910 and available from https://doi.org/10.5281/zenodo.20283378. + description: Molecular dynamics trajectory of a lipid bilayer of 40 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) + at 303.15 K. Simulated with CHARMM36 in GROMACS 2026.1 for 100 ns (8800 atoms). + Deposited as NMRlipids Databank simulation 910 and available from https://doi.org/10.5281/zenodo.20283378. sameAs: https://doi.org/10.5281/zenodo.20283378 datePublished: '2026-06-03' license: @@ -141,7 +144,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.20283378 identifier: 10.5281/zenodo.20283378 url: https://doi.org/10.5281/zenodo.20283378 - name: MD simulation trajectory and related files for DMPC lipid bilayer in full hydration at 303 K with Charmm6 + name: MD simulation trajectory and related files for DMPC lipid bilayer in full + hydration at 303 K with Charmm6 publisher: Zenodo _source: api: datacite diff --git a/Simulations/cf1/3f5/cf13f50e4136d05074843ec1e2d92311a6caec5f/e6988d53abcfd89b5bfff6b523d43ea4ff9791a1/README.yaml b/Simulations/cf1/3f5/cf13f50e4136d05074843ec1e2d92311a6caec5f/e6988d53abcfd89b5bfff6b523d43ea4ff9791a1/README.yaml index 73cf85090a..550c06eac0 100644 --- a/Simulations/cf1/3f5/cf13f50e4136d05074843ec1e2d92311a6caec5f/e6988d53abcfd89b5bfff6b523d43ea4ff9791a1/README.yaml +++ b/Simulations/cf1/3f5/cf13f50e4136d05074843ec1e2d92311a6caec5f/e6988d53abcfd89b5bfff6b523d43ea4ff9791a1/README.yaml @@ -46,9 +46,12 @@ EXPERIMENT: - 10.1016/j.bbamem.2011.07.022/11 ID: 103 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 313 K (ECC-lipids, GROMACS 5.1.4, 200 ns) [NMRlipids simulation 103] + name: Molecular dynamics trajectory of a POPC bilayer at 313 K (ECC-lipids, GROMACS + 5.1.4, 200 ns) [NMRlipids simulation 103] alternateName: 128POPC_6400SOL_313K_TIP4p2005model - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 200 ns (42752 atoms). Deposited as NMRlipids Databank simulation 103 and available from https://doi.org/10.5281/zenodo.1118980. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 200 ns (42752 atoms). + Deposited as NMRlipids Databank simulation 103 and available from https://doi.org/10.5281/zenodo.1118980. sameAs: https://doi.org/10.5281/zenodo.1118980 datePublished: '2017-12-19' license: @@ -138,7 +141,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1118980 identifier: 10.5281/zenodo.1118980 url: https://doi.org/10.5281/zenodo.1118980 - name: Simulations Of Popc Lipid Bilayer In Water Solution At Various Nacl And Cacl2 Concentrations Using Ecc-Popc Force Field And Various Water Models + name: Simulations Of Popc Lipid Bilayer In Water Solution At Various Nacl And + Cacl2 Concentrations Using Ecc-Popc Force Field And Various Water Models publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/cf4/038/cf4038c468bcdc08de31d430c456422fe5e7e0bc/6677606cb33c86fe79b9b9ba19e481f2d5388e1c/README.yaml b/Simulations/cf4/038/cf4038c468bcdc08de31d430c456422fe5e7e0bc/6677606cb33c86fe79b9b9ba19e481f2d5388e1c/README.yaml index 736bfcd9a7..41dc4951e3 100644 --- a/Simulations/cf4/038/cf4038c468bcdc08de31d430c456422fe5e7e0bc/6677606cb33c86fe79b9b9ba19e481f2d5388e1c/README.yaml +++ b/Simulations/cf4/038/cf4038c468bcdc08de31d430c456422fe5e7e0bc/6677606cb33c86fe79b9b9ba19e481f2d5388e1c/README.yaml @@ -44,9 +44,12 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 563 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 303.15 K (CHARMM36, GROMACS 5.1.2, 60 ns) [NMRlipids simulation 563] + name: Molecular dynamics trajectory of a POPC bilayer at 303.15 K (CHARMM36, GROMACS + 5.1.2, 60 ns) [NMRlipids simulation 563] alternateName: 128POPC_5120SOL_303K - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 303.15 K. Simulated with CHARMM36 in GROMACS 5.1.2 for 60 ns (32512 atoms). Deposited as NMRlipids Databank simulation 563 and available from https://doi.org/10.5281/zenodo.153944. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 303.15 K. Simulated with CHARMM36 in GROMACS 5.1.2 for 60 ns (32512 atoms). + Deposited as NMRlipids Databank simulation 563 and available from https://doi.org/10.5281/zenodo.153944. sameAs: https://doi.org/10.5281/zenodo.153944 datePublished: '2016-09-13' license: @@ -139,7 +142,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.153944 identifier: 10.5281/zenodo.153944 url: https://doi.org/10.5281/zenodo.153944 - name: Popc Lipid Membrane, 303K, Charmm36 Force Field, Simulation Files And 200 Ns Trajectory For Gromacs Md Simulation Engine V5.1.2 + name: Popc Lipid Membrane, 303K, Charmm36 Force Field, Simulation Files And 200 + Ns Trajectory For Gromacs Md Simulation Engine V5.1.2 publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/cf4/20a/cf420a356ed12c3697465d9933876dfbef382e98/cf420a356ed12c3697465d9933876dfbef382e98/README.yaml b/Simulations/cf4/20a/cf420a356ed12c3697465d9933876dfbef382e98/cf420a356ed12c3697465d9933876dfbef382e98/README.yaml index 5871a85e9c..1d2ef62c6d 100644 --- a/Simulations/cf4/20a/cf420a356ed12c3697465d9933876dfbef382e98/cf420a356ed12c3697465d9933876dfbef382e98/README.yaml +++ b/Simulations/cf4/20a/cf420a356ed12c3697465d9933876dfbef382e98/cf420a356ed12c3697465d9933876dfbef382e98/README.yaml @@ -37,9 +37,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 562 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 303 K (Charmm-Drude polarizable, OPENMM 7.4.1, 2 ns) [NMRlipids simulation 562] + name: Molecular dynamics trajectory of a POPC bilayer at 303 K (Charmm-Drude polarizable, + OPENMM 7.4.1, 2 ns) [NMRlipids simulation 562] alternateName: 72POPC_303K (equilibriated using Charmm36) - description: Molecular dynamics trajectory of a lipid bilayer of 72 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 303 K. Simulated with Charmm-Drude polarizable in OPENMM 7.4.1 for 2 ns (13968 atoms). Deposited as NMRlipids Databank simulation 562 and available from https://doi.org/10.5281/zenodo.3865283. + description: Molecular dynamics trajectory of a lipid bilayer of 72 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 303 K. Simulated with Charmm-Drude polarizable in OPENMM 7.4.1 for 2 ns (13968 + atoms). Deposited as NMRlipids Databank simulation 562 and available from https://doi.org/10.5281/zenodo.3865283. sameAs: https://doi.org/10.5281/zenodo.3865283 datePublished: '2020-05-29' license: diff --git a/Simulations/cf8/595/cf8595ddf06ded7c0ebc34647c1998fe50c09ca8/cf8595ddf06ded7c0ebc34647c1998fe50c09ca8/README.yaml b/Simulations/cf8/595/cf8595ddf06ded7c0ebc34647c1998fe50c09ca8/cf8595ddf06ded7c0ebc34647c1998fe50c09ca8/README.yaml index 454520c20f..d9258a35a9 100644 --- a/Simulations/cf8/595/cf8595ddf06ded7c0ebc34647c1998fe50c09ca8/cf8595ddf06ded7c0ebc34647c1998fe50c09ca8/README.yaml +++ b/Simulations/cf8/595/cf8595ddf06ded7c0ebc34647c1998fe50c09ca8/cf8595ddf06ded7c0ebc34647c1998fe50c09ca8/README.yaml @@ -46,9 +46,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 745 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (45:27:27) bilayer at 303 K (Charmm-Drude polarizable; system has been equilibriated using Charmm36, OPENMM 7.4.1, 513 ns) [NMRlipids simulation 745] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (45:27:27) bilayer at 303 + K (Charmm-Drude polarizable; system has been equilibriated using Charmm36, OPENMM + 7.4.1, 513 ns) [NMRlipids simulation 745] alternateName: 128POPC_6400SOL_77NaCl_303K - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 45 mol%), 77 CLA (27 mol%) and 77 SOD (27 mol%) at 303 K. Simulated with Charmm-Drude polarizable; system has been equilibriated using Charmm36 in OPENMM 7.4.1 for 513 ns (57140 atoms). Deposited as NMRlipids Databank simulation 745 and available from https://doi.org/10.5281/zenodo.7596011. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 45 mol%), 77 CLA (27 mol%) and 77 SOD (27 mol%) at 303 K. Simulated with Charmm-Drude + polarizable; system has been equilibriated using Charmm36 in OPENMM 7.4.1 for + 513 ns (57140 atoms). Deposited as NMRlipids Databank simulation 745 and available + from https://doi.org/10.5281/zenodo.7596011. sameAs: https://doi.org/10.5281/zenodo.7596011 datePublished: '2020-08-19' license: @@ -140,7 +146,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.7596011 identifier: 10.5281/zenodo.7596011 url: https://doi.org/10.5281/zenodo.7596011 - name: Pure POPC Membrane with 650mM NaCl simulations using Drude Polarizable Force Field and OpenMM + name: Pure POPC Membrane with 650mM NaCl simulations using Drude Polarizable Force + Field and OpenMM publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/cfb/a18/cfba18cb6fbbc3ce348e83cc27dead0472882f17/53a843832460b6e8320a71cad1a51ef0a49b3f06/README.yaml b/Simulations/cfb/a18/cfba18cb6fbbc3ce348e83cc27dead0472882f17/53a843832460b6e8320a71cad1a51ef0a49b3f06/README.yaml index d53c0707e4..6f25b76ada 100644 --- a/Simulations/cfb/a18/cfba18cb6fbbc3ce348e83cc27dead0472882f17/53a843832460b6e8320a71cad1a51ef0a49b3f06/README.yaml +++ b/Simulations/cfb/a18/cfba18cb6fbbc3ce348e83cc27dead0472882f17/53a843832460b6e8320a71cad1a51ef0a49b3f06/README.yaml @@ -40,9 +40,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 519 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 298 K (MacRog, GROMACS 4.5.5, 50 ns) [NMRlipids simulation 519] + name: Molecular dynamics trajectory of a POPC bilayer at 298 K (MacRog, GROMACS + 4.5.5, 50 ns) [NMRlipids simulation 519] alternateName: 288POPC_7200SOL_298K - description: Molecular dynamics trajectory of a lipid bilayer of 288 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 298 K. Simulated with MacRog in GROMACS 4.5.5 for 50 ns (60192 atoms). Deposited as NMRlipids Databank simulation 519 and available from https://doi.org/10.5281/zenodo.13498. + description: Molecular dynamics trajectory of a lipid bilayer of 288 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 298 K. Simulated with MacRog in GROMACS 4.5.5 for 50 ns (60192 atoms). Deposited + as NMRlipids Databank simulation 519 and available from https://doi.org/10.5281/zenodo.13498. sameAs: https://doi.org/10.5281/zenodo.13498 datePublished: '2014-12-30' license: diff --git a/Simulations/cfc/4c4/cfc4c4be95331177929f47a2f1c59f2792643901/112cf0742e84e4dbdd3598c8bcc6921f84378fb3/README.yaml b/Simulations/cfc/4c4/cfc4c4be95331177929f47a2f1c59f2792643901/112cf0742e84e4dbdd3598c8bcc6921f84378fb3/README.yaml index cc3ab5c00e..ca39236474 100644 --- a/Simulations/cfc/4c4/cfc4c4be95331177929f47a2f1c59f2792643901/112cf0742e84e4dbdd3598c8bcc6921f84378fb3/README.yaml +++ b/Simulations/cfc/4c4/cfc4c4be95331177929f47a2f1c59f2792643901/112cf0742e84e4dbdd3598c8bcc6921f84378fb3/README.yaml @@ -55,9 +55,15 @@ EXPERIMENT: ID: 363 AUTHORS_CONTACT: Kiirikki, M. Anne; Ollila O. H. Samuli bioschema_properties: - name: Molecular dynamics trajectory of a CLA/CAL/POPC/POPG/SOD (49:24:18:5:5) bilayer at 298 K (lipid17ecc, GROMACS, 300 ns) [NMRlipids simulation 363] + name: Molecular dynamics trajectory of a CLA/CAL/POPC/POPG/SOD (49:24:18:5:5) bilayer + at 298 K (lipid17ecc, GROMACS, 300 ns) [NMRlipids simulation 363] alternateName: POPC:POPG(4:1)_T298K_1MCaCl - description: Molecular dynamics trajectory of a lipid bilayer of 950 CLA (49 mol%), 475 CAL (24 mol%), 350 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 18 mol%), 88 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 5 mol%) and 88 SOD (5 mol%) at 298 K. Simulated with lipid17ecc in GROMACS for 300 ns (134109 atoms). Deposited as NMRlipids Databank simulation 363 and available from https://doi.org/10.5281/zenodo.3997184. + description: Molecular dynamics trajectory of a lipid bilayer of 950 CLA (49 mol%), + 475 CAL (24 mol%), 350 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 18 mol%), 88 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 5 mol%) + and 88 SOD (5 mol%) at 298 K. Simulated with lipid17ecc in GROMACS for 300 ns + (134109 atoms). Deposited as NMRlipids Databank simulation 363 and available from + https://doi.org/10.5281/zenodo.3997184. sameAs: https://doi.org/10.5281/zenodo.3997184 datePublished: '2020-08-24' license: @@ -147,7 +153,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3997184 identifier: 10.5281/zenodo.3997184 url: https://doi.org/10.5281/zenodo.3997184 - name: Lipid17ecc POPC:POPG 4:1 bilayer simulation in 1 M CaCl2 solution and Na+ counter ions + name: Lipid17ecc POPC:POPG 4:1 bilayer simulation in 1 M CaCl2 solution and Na+ + counter ions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/cfe/023/cfe023f459a3c0c0a6cba3d5b0dfcee23176bf5d/cfe023f459a3c0c0a6cba3d5b0dfcee23176bf5d/README.yaml b/Simulations/cfe/023/cfe023f459a3c0c0a6cba3d5b0dfcee23176bf5d/cfe023f459a3c0c0a6cba3d5b0dfcee23176bf5d/README.yaml index 746a18f365..5f76f08718 100644 --- a/Simulations/cfe/023/cfe023f459a3c0c0a6cba3d5b0dfcee23176bf5d/cfe023f459a3c0c0a6cba3d5b0dfcee23176bf5d/README.yaml +++ b/Simulations/cfe/023/cfe023f459a3c0c0a6cba3d5b0dfcee23176bf5d/cfe023f459a3c0c0a6cba3d5b0dfcee23176bf5d/README.yaml @@ -59,9 +59,14 @@ EXPERIMENT: TOCL: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a POPG/POT/DPPGK/CLA/TOCL (40:27:23:7:3) bilayer at 303 K (Charmm36, OPENMM 7.5.1, 500 ns) [NMRlipids simulation 782] + name: Molecular dynamics trajectory of a POPG/POT/DPPGK/CLA/TOCL (40:27:23:7:3) + bilayer at 303 K (Charmm36, OPENMM 7.5.1, 500 ns) [NMRlipids simulation 782] alternateName: Gram-positive bilayer membrane (60% PG, 35% lysyl-PG, 5% CL) - description: Molecular dynamics trajectory of a lipid bilayer of 96 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 40 mol%), 64 POT (27 mol%), 56 DPPGK (1,2-dioleoyl-sn-glycero-3-[phospho-rac-(3-lysyl(1-glycerol))] (lysyl-PG), 23 mol%), 16 CLA (7 mol%) and 8 TOCL (1’,3’-Bis[1,2-dioleoyl-sn-glycero-3-phospho]-glycerol, 3 mol%) at 303 K. Simulated with Charmm36 in OPENMM 7.5.1 for 500 ns (42576 atoms). Deposited as NMRlipids Databank simulation 782 and available from https://doi.org/10.5281/zenodo.8415046. + description: Molecular dynamics trajectory of a lipid bilayer of 96 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, + 40 mol%), 64 POT (27 mol%), 56 DPPGK (1,2-dioleoyl-sn-glycero-3-[phospho-rac-(3-lysyl(1-glycerol))] + (lysyl-PG), 23 mol%), 16 CLA (7 mol%) and 8 TOCL (1’,3’-Bis[1,2-dioleoyl-sn-glycero-3-phospho]-glycerol, + 3 mol%) at 303 K. Simulated with Charmm36 in OPENMM 7.5.1 for 500 ns (42576 atoms). + Deposited as NMRlipids Databank simulation 782 and available from https://doi.org/10.5281/zenodo.8415046. sameAs: https://doi.org/10.5281/zenodo.8415046 datePublished: '2023-10-06' license: @@ -153,7 +158,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.8415046 identifier: 10.5281/zenodo.8415046 url: https://doi.org/10.5281/zenodo.8415046 - name: MD simulation of a model Gram-positive bilayer membrane (60% PG, 35% lysyl-PG, 5% CL) + name: MD simulation of a model Gram-positive bilayer membrane (60% PG, 35% lysyl-PG, + 5% CL) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/d05/91a/d0591a5a15bc34c6ae88afbb9ceaeceab4b10f61/1b5cbfbb7d3616c67175060eabd54b32f59d7c3c/README.yaml b/Simulations/d05/91a/d0591a5a15bc34c6ae88afbb9ceaeceab4b10f61/1b5cbfbb7d3616c67175060eabd54b32f59d7c3c/README.yaml index b3f9231d5b..1ab453665f 100644 --- a/Simulations/d05/91a/d0591a5a15bc34c6ae88afbb9ceaeceab4b10f61/1b5cbfbb7d3616c67175060eabd54b32f59d7c3c/README.yaml +++ b/Simulations/d05/91a/d0591a5a15bc34c6ae88afbb9ceaeceab4b10f61/1b5cbfbb7d3616c67175060eabd54b32f59d7c3c/README.yaml @@ -63,9 +63,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 621 bioschema_properties: - name: Molecular dynamics trajectory of a SOD/POPC/CLA/POPS (34:32:25:8) bilayer at 310 K (Berger, GROMACS 4.0.7, 50 ns) [NMRlipids simulation 621] + name: Molecular dynamics trajectory of a SOD/POPC/CLA/POPS (34:32:25:8) bilayer + at 310 K (Berger, GROMACS 4.0.7, 50 ns) [NMRlipids simulation 621] alternateName: 102POPC_26POPS_4290SOL_106SOD_80CLA_310K_Berger - description: Molecular dynamics trajectory of a lipid bilayer of 106 SOD (34 mol%), 102 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 32 mol%), 80 CLA (25 mol%) and 26 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 8 mol%) at 310 K. Simulated with Berger in GROMACS 4.0.7 for 50 ns (19790 atoms). Deposited as NMRlipids Databank simulation 621 and available from https://doi.org/10.5281/zenodo.838219. + description: Molecular dynamics trajectory of a lipid bilayer of 106 SOD (34 mol%), + 102 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 32 mol%), 80 CLA (25 + mol%) and 26 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 8 mol%) + at 310 K. Simulated with Berger in GROMACS 4.0.7 for 50 ns (19790 atoms). Deposited + as NMRlipids Databank simulation 621 and available from https://doi.org/10.5281/zenodo.838219. sameAs: https://doi.org/10.5281/zenodo.838219 datePublished: '2017-08-02' license: @@ -158,7 +163,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.838219 identifier: 10.5281/zenodo.838219 url: https://doi.org/10.5281/zenodo.838219 - name: Md Simulation Trajectory Of A Popc/Pops (4:1) Bilayer With 1M Nacl, Berger Force Field For Lipids And Ffgmx For Ions + name: Md Simulation Trajectory Of A Popc/Pops (4:1) Bilayer With 1M Nacl, Berger + Force Field For Lipids And Ffgmx For Ions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/d09/793/d0979303cb75633a1da05a7fc3a60af9205daacf/8e123ad75ec712b0a35ea1f5532820d0cb55dc6e/README.yaml b/Simulations/d09/793/d0979303cb75633a1da05a7fc3a60af9205daacf/8e123ad75ec712b0a35ea1f5532820d0cb55dc6e/README.yaml index a5592a8d2d..546cfab3c7 100644 --- a/Simulations/d09/793/d0979303cb75633a1da05a7fc3a60af9205daacf/8e123ad75ec712b0a35ea1f5532820d0cb55dc6e/README.yaml +++ b/Simulations/d09/793/d0979303cb75633a1da05a7fc3a60af9205daacf/8e123ad75ec712b0a35ea1f5532820d0cb55dc6e/README.yaml @@ -51,9 +51,13 @@ EXPERIMENT: CHOL: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a DOPC/CHOL (62:38) bilayer at 333.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 653] + name: Molecular dynamics trajectory of a DOPC/CHOL (62:38) bilayer at 333.15 K (CHARMM36, + GROMACS, 1001 ns) [NMRlipids simulation 653] alternateName: 256DOPC_160CHOL_20800SOL_333K - description: Molecular dynamics trajectory of a lipid bilayer of 256 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, 62 mol%) and 160 CHOL (cholesterol, 38 mol%) at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (109568 atoms). Deposited as NMRlipids Databank simulation 653 and available from https://doi.org/10.5281/zenodo.6943929. + description: Molecular dynamics trajectory of a lipid bilayer of 256 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, + 62 mol%) and 160 CHOL (cholesterol, 38 mol%) at 333.15 K. Simulated with CHARMM36 + in GROMACS for 1001 ns (109568 atoms). Deposited as NMRlipids Databank simulation + 653 and available from https://doi.org/10.5281/zenodo.6943929. sameAs: https://doi.org/10.5281/zenodo.6943929 datePublished: '2022-07-30' license: diff --git a/Simulations/d0a/acf/d0aacf2392a074c84c540c30058708ec75394c32/64c2fa23c30e1f8471d6686ac85846875094a9d4/README.yaml b/Simulations/d0a/acf/d0aacf2392a074c84c540c30058708ec75394c32/64c2fa23c30e1f8471d6686ac85846875094a9d4/README.yaml index 6486820d9b..a5d839e57b 100644 --- a/Simulations/d0a/acf/d0aacf2392a074c84c540c30058708ec75394c32/64c2fa23c30e1f8471d6686ac85846875094a9d4/README.yaml +++ b/Simulations/d0a/acf/d0aacf2392a074c84c540c30058708ec75394c32/64c2fa23c30e1f8471d6686ac85846875094a9d4/README.yaml @@ -53,9 +53,13 @@ EXPERIMENT: - 10.1039/C4SM00066H/3 ID: 425 bioschema_properties: - name: Molecular dynamics trajectory of a POPS/SOD (50:50) bilayer at 298 K (GROMOS-CKP, GROMOS NH3 charges and PME, GROMACS, 100 ns) [NMRlipids simulation 425] + name: Molecular dynamics trajectory of a POPS/SOD (50:50) bilayer at 298 K (GROMOS-CKP, + GROMOS NH3 charges and PME, GROMACS, 100 ns) [NMRlipids simulation 425] alternateName: 128POPS_4480SOL_128SOD_298K_GROMOS-CKP_v1 - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 50 mol%) and 128 SOD (50 mol%) at 298 K. Simulated with GROMOS-CKP, GROMOS NH3 charges and PME in GROMACS for 100 ns (20608 atoms). Deposited as NMRlipids Databank simulation 425 and available from https://doi.org/10.5281/zenodo.1129435. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, + 50 mol%) and 128 SOD (50 mol%) at 298 K. Simulated with GROMOS-CKP, GROMOS NH3 + charges and PME in GROMACS for 100 ns (20608 atoms). Deposited as NMRlipids Databank + simulation 425 and available from https://doi.org/10.5281/zenodo.1129435. sameAs: https://doi.org/10.5281/zenodo.1129435 datePublished: '2017-12-24' license: @@ -148,7 +152,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1129435 identifier: 10.5281/zenodo.1129435 url: https://doi.org/10.5281/zenodo.1129435 - name: Gromos-Ckp Pops Simulations (Versions 1 And 2) 298 K With Gromos Nh3 Charges And Pme + name: Gromos-Ckp Pops Simulations (Versions 1 And 2) 298 K With Gromos Nh3 Charges + And Pme publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/d0c/cca/d0cccab96a52325d65e1be3e59706c5215911089/5dd86a4c1e65de95673d1f5ebdc685d6eb1fc155/README.yaml b/Simulations/d0c/cca/d0cccab96a52325d65e1be3e59706c5215911089/5dd86a4c1e65de95673d1f5ebdc685d6eb1fc155/README.yaml index 123407b44b..52d7dd5b73 100644 --- a/Simulations/d0c/cca/d0cccab96a52325d65e1be3e59706c5215911089/5dd86a4c1e65de95673d1f5ebdc685d6eb1fc155/README.yaml +++ b/Simulations/d0c/cca/d0cccab96a52325d65e1be3e59706c5215911089/5dd86a4c1e65de95673d1f5ebdc685d6eb1fc155/README.yaml @@ -50,9 +50,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 280 bioschema_properties: - name: Molecular dynamics trajectory of a CHOL/POPC (50:50) bilayer at 303.15 K (CHARMM36, GROMACS 5, 86 ns) [NMRlipids simulation 280] + name: Molecular dynamics trajectory of a CHOL/POPC (50:50) bilayer at 303.15 K (CHARMM36, + GROMACS 5, 86 ns) [NMRlipids simulation 280] alternateName: 80POPC_7200SOL_80CHOL_303.80K - description: Molecular dynamics trajectory of a lipid bilayer of 80 CHOL (cholesterol, 50 mol%) and 80 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 50 mol%) at 303.15 K. Simulated with CHARMM36 in GROMACS 5 for 86 ns (38240 atoms). Deposited as NMRlipids Databank simulation 280 and available from https://doi.org/10.5281/zenodo.247386. + description: Molecular dynamics trajectory of a lipid bilayer of 80 CHOL (cholesterol, + 50 mol%) and 80 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 50 mol%) + at 303.15 K. Simulated with CHARMM36 in GROMACS 5 for 86 ns (38240 atoms). Deposited + as NMRlipids Databank simulation 280 and available from https://doi.org/10.5281/zenodo.247386. sameAs: https://doi.org/10.5281/zenodo.247386 datePublished: '2017-01-16' license: @@ -142,7 +146,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.247386 identifier: 10.5281/zenodo.247386 url: https://doi.org/10.5281/zenodo.247386 - name: Popc/Cholesterol (50:50) Lipid Membrane, 303K, Charmm36 Force Field, Simulation Files And 100 Ns Trajectory For Gromacs Simulation Engine V5 + name: Popc/Cholesterol (50:50) Lipid Membrane, 303K, Charmm36 Force Field, Simulation + Files And 100 Ns Trajectory For Gromacs Simulation Engine V5 publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/d15/255/d152552d182b9d3b623ca5cc03700fef00505b05/f7dd41f2428fbc621fed20aefa8cceafaf761d53/README.yaml b/Simulations/d15/255/d152552d182b9d3b623ca5cc03700fef00505b05/f7dd41f2428fbc621fed20aefa8cceafaf761d53/README.yaml index 7fca545b87..484a2a6c02 100644 --- a/Simulations/d15/255/d152552d182b9d3b623ca5cc03700fef00505b05/f7dd41f2428fbc621fed20aefa8cceafaf761d53/README.yaml +++ b/Simulations/d15/255/d152552d182b9d3b623ca5cc03700fef00505b05/f7dd41f2428fbc621fed20aefa8cceafaf761d53/README.yaml @@ -49,9 +49,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 488 bioschema_properties: - name: Molecular dynamics trajectory of a CHOL/POPC (50:50) bilayer at 310 K (CHARMM36, GROMACS, 500 ns) [NMRlipids simulation 488] + name: Molecular dynamics trajectory of a CHOL/POPC (50:50) bilayer at 310 K (CHARMM36, + GROMACS, 500 ns) [NMRlipids simulation 488] alternateName: 200POPC_200CHOL_18000SOL_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 CHOL (cholesterol, 50 mol%) and 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 50 mol%) at 310 K. Simulated with CHARMM36 in GROMACS for 500 ns (95600 atoms). Deposited as NMRlipids Databank simulation 488 and available from https://doi.org/10.5281/zenodo.3238157. + description: Molecular dynamics trajectory of a lipid bilayer of 200 CHOL (cholesterol, + 50 mol%) and 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 50 mol%) + at 310 K. Simulated with CHARMM36 in GROMACS for 500 ns (95600 atoms). Deposited + as NMRlipids Databank simulation 488 and available from https://doi.org/10.5281/zenodo.3238157. sameAs: https://doi.org/10.5281/zenodo.3238157 datePublished: '2016-09-08' license: diff --git a/Simulations/d17/7fd/d177fd5fedadcdcdef9e0250f72a0ef6a7136373/b727eb1330fc16c256ca4b528be9cad809322259/README.yaml b/Simulations/d17/7fd/d177fd5fedadcdcdef9e0250f72a0ef6a7136373/b727eb1330fc16c256ca4b528be9cad809322259/README.yaml index 5d793291ab..7470b00367 100644 --- a/Simulations/d17/7fd/d177fd5fedadcdcdef9e0250f72a0ef6a7136373/b727eb1330fc16c256ca4b528be9cad809322259/README.yaml +++ b/Simulations/d17/7fd/d177fd5fedadcdcdef9e0250f72a0ef6a7136373/b727eb1330fc16c256ca4b528be9cad809322259/README.yaml @@ -41,9 +41,12 @@ EXPERIMENT: FORMFACTOR: - 10.1021/acs.jctc.3c00648/1 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 300 K (OpenFF, GROMACS, 200 ns) [NMRlipids simulation 792] + name: Molecular dynamics trajectory of a POPC bilayer at 300 K (OpenFF, GROMACS, + 200 ns) [NMRlipids simulation 792] alternateName: POPC_128_OPENFF_300K - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 300 K. Simulated with OpenFF in GROMACS for 200 ns (32152 atoms). Deposited as NMRlipids Databank simulation 792 and available from https://doi.org/10.5281/zenodo.8411425. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 300 K. Simulated with OpenFF in GROMACS for 200 ns (32152 atoms). Deposited + as NMRlipids Databank simulation 792 and available from https://doi.org/10.5281/zenodo.8411425. sameAs: https://doi.org/10.5281/zenodo.8411425 datePublished: '2023-10-05' license: diff --git a/Simulations/d1b/fe4/d1bfe472aaefaa4991e8b6ddb3a888cdeeb6a7ad/870f1ea073265c465676161147d9037a9a2253e3/README.yaml b/Simulations/d1b/fe4/d1bfe472aaefaa4991e8b6ddb3a888cdeeb6a7ad/870f1ea073265c465676161147d9037a9a2253e3/README.yaml index 47da31c998..676d7351fd 100644 --- a/Simulations/d1b/fe4/d1bfe472aaefaa4991e8b6ddb3a888cdeeb6a7ad/870f1ea073265c465676161147d9037a9a2253e3/README.yaml +++ b/Simulations/d1b/fe4/d1bfe472aaefaa4991e8b6ddb3a888cdeeb6a7ad/870f1ea073265c465676161147d9037a9a2253e3/README.yaml @@ -45,9 +45,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 101 bioschema_properties: - name: Molecular dynamics trajectory of a DLPC bilayer at 300 K (Berger-DLPC-13, GROMACS 4.5.4, 80 ns) [NMRlipids simulation 101] + name: Molecular dynamics trajectory of a DLPC bilayer at 300 K (Berger-DLPC-13, + GROMACS 4.5.4, 80 ns) [NMRlipids simulation 101] alternateName: 72DLPC_1440SOL_300K - description: Molecular dynamics trajectory of a lipid bilayer of 72 DLPC (1,2-dilauroyl-sn-glycero-3-phosphocholine) at 300 K. Simulated with Berger-DLPC-13 in GROMACS 4.5.4 for 80 ns (7344 atoms). Deposited as NMRlipids Databank simulation 101 and available from https://doi.org/10.5281/zenodo.16291. + description: Molecular dynamics trajectory of a lipid bilayer of 72 DLPC (1,2-dilauroyl-sn-glycero-3-phosphocholine) + at 300 K. Simulated with Berger-DLPC-13 in GROMACS 4.5.4 for 80 ns (7344 atoms). + Deposited as NMRlipids Databank simulation 101 and available from https://doi.org/10.5281/zenodo.16291. sameAs: https://doi.org/10.5281/zenodo.16291 datePublished: '2015-03-24' license: diff --git a/Simulations/d2d/e84/d2de846440bb44943576a453c16fe2fecb72dd35/5543261238b28a18b72d642786f24805a835c046/README.yaml b/Simulations/d2d/e84/d2de846440bb44943576a453c16fe2fecb72dd35/5543261238b28a18b72d642786f24805a835c046/README.yaml index 3d34644a5d..7d5b5d15b0 100644 --- a/Simulations/d2d/e84/d2de846440bb44943576a453c16fe2fecb72dd35/5543261238b28a18b72d642786f24805a835c046/README.yaml +++ b/Simulations/d2d/e84/d2de846440bb44943576a453c16fe2fecb72dd35/5543261238b28a18b72d642786f24805a835c046/README.yaml @@ -45,9 +45,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 81 bioschema_properties: - name: Molecular dynamics trajectory of a DLPC bilayer at 300 K (Berger-DLPC-13, GROMACS 4.5.4, 80 ns) [NMRlipids simulation 81] + name: Molecular dynamics trajectory of a DLPC bilayer at 300 K (Berger-DLPC-13, + GROMACS 4.5.4, 80 ns) [NMRlipids simulation 81] alternateName: 72DLPC_288SOL_300K - description: Molecular dynamics trajectory of a lipid bilayer of 72 DLPC (1,2-dilauroyl-sn-glycero-3-phosphocholine) at 300 K. Simulated with Berger-DLPC-13 in GROMACS 4.5.4 for 80 ns (3888 atoms). Deposited as NMRlipids Databank simulation 81 and available from https://doi.org/10.5281/zenodo.16295. + description: Molecular dynamics trajectory of a lipid bilayer of 72 DLPC (1,2-dilauroyl-sn-glycero-3-phosphocholine) + at 300 K. Simulated with Berger-DLPC-13 in GROMACS 4.5.4 for 80 ns (3888 atoms). + Deposited as NMRlipids Databank simulation 81 and available from https://doi.org/10.5281/zenodo.16295. sameAs: https://doi.org/10.5281/zenodo.16295 datePublished: '2015-03-24' license: diff --git a/Simulations/d32/985/d32985a494379d6aabd2ddea8c0b18fefe485826/d4b2a35659ef386736bf0f149607413532d34bbe/README.yaml b/Simulations/d32/985/d32985a494379d6aabd2ddea8c0b18fefe485826/d4b2a35659ef386736bf0f149607413532d34bbe/README.yaml index 80250a335d..79098c9adf 100644 --- a/Simulations/d32/985/d32985a494379d6aabd2ddea8c0b18fefe485826/d4b2a35659ef386736bf0f149607413532d34bbe/README.yaml +++ b/Simulations/d32/985/d32985a494379d6aabd2ddea8c0b18fefe485826/d4b2a35659ef386736bf0f149607413532d34bbe/README.yaml @@ -54,9 +54,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 336 bioschema_properties: - name: Molecular dynamics trajectory of a CLA/DHMDMAB/POPC (33:33:33) bilayer at 313 K (Lipid14, GROMACS, 180 ns) [NMRlipids simulation 336] + name: Molecular dynamics trajectory of a CLA/DHMDMAB/POPC (33:33:33) bilayer at + 313 K (Lipid14, GROMACS, 180 ns) [NMRlipids simulation 336] alternateName: 100POPC_100DHMDMAB_6214SOL_100CLA_313K - description: Molecular dynamics trajectory of a lipid bilayer of 100 CLA (33 mol%), 100 DHMDMAB (dihexadecyldimethylammonium, 33 mol%) and 100 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 33 mol%) at 313 K. Simulated with Lipid14 in GROMACS for 180 ns (42842 atoms). Deposited as NMRlipids Databank simulation 336 and available from https://doi.org/10.5281/zenodo.1020689. + description: Molecular dynamics trajectory of a lipid bilayer of 100 CLA (33 mol%), + 100 DHMDMAB (dihexadecyldimethylammonium, 33 mol%) and 100 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 33 mol%) at 313 K. Simulated with Lipid14 in GROMACS for 180 ns (42842 atoms). + Deposited as NMRlipids Databank simulation 336 and available from https://doi.org/10.5281/zenodo.1020689. sameAs: https://doi.org/10.5281/zenodo.1020689 datePublished: '2017-10-18' license: @@ -145,7 +149,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1020689 identifier: 10.5281/zenodo.1020689 url: https://doi.org/10.5281/zenodo.1020689 - name: Popc Bilayer With 50% Of Dihexadecyldimethylammonium Simulated At T313K With The Lipid14 Model Using Gromacs + name: Popc Bilayer With 50% Of Dihexadecyldimethylammonium Simulated At T313K + With The Lipid14 Model Using Gromacs publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/d33/115/d3311502915a88e4d83d8099564172d4d8c11b55/d3311502915a88e4d83d8099564172d4d8c11b55/README.yaml b/Simulations/d33/115/d3311502915a88e4d83d8099564172d4d8c11b55/d3311502915a88e4d83d8099564172d4d8c11b55/README.yaml index bae1b082f3..c6e05cab15 100644 --- a/Simulations/d33/115/d3311502915a88e4d83d8099564172d4d8c11b55/d3311502915a88e4d83d8099564172d4d8c11b55/README.yaml +++ b/Simulations/d33/115/d3311502915a88e4d83d8099564172d4d8c11b55/d3311502915a88e4d83d8099564172d4d8c11b55/README.yaml @@ -50,9 +50,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 732 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (36:32:32) bilayer at 303 K (Charmm-Drude polarizable; system has been equilibriated using Charmm36, OPENMM 7.4.1, 475 ns) [NMRlipids simulation 732] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (36:32:32) bilayer at 303 + K (Charmm-Drude polarizable; system has been equilibriated using Charmm36, OPENMM + 7.4.1, 475 ns) [NMRlipids simulation 732] alternateName: 128POPC_6400SOL_115NaCl_303K - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 36 mol%), 115 CLA (32 mol%) and 115 SOD (32 mol%) at 303 K. Simulated with Charmm-Drude polarizable; system has been equilibriated using Charmm36 in OPENMM 7.4.1 for 475 ns (57292 atoms). Deposited as NMRlipids Databank simulation 732 and available from https://doi.org/10.5281/zenodo.7600326. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 36 mol%), 115 CLA (32 mol%) and 115 SOD (32 mol%) at 303 K. Simulated with Charmm-Drude + polarizable; system has been equilibriated using Charmm36 in OPENMM 7.4.1 for + 475 ns (57292 atoms). Deposited as NMRlipids Databank simulation 732 and available + from https://doi.org/10.5281/zenodo.7600326. sameAs: https://doi.org/10.5281/zenodo.7600326 datePublished: '2020-08-19' license: @@ -144,7 +150,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.7600326 identifier: 10.5281/zenodo.7600326 url: https://doi.org/10.5281/zenodo.7600326 - name: Pure POPC Membrane with 1000mM NaCl simulations using Drude Polarizable Force Field and OpenMM + name: Pure POPC Membrane with 1000mM NaCl simulations using Drude Polarizable + Force Field and OpenMM publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/d34/73d/d3473d6d3560f722e43a5715b8eafba1192e809f/5e83fee5980f5362fc7bf56d3341d183aa9b13fd/README.yaml b/Simulations/d34/73d/d3473d6d3560f722e43a5715b8eafba1192e809f/5e83fee5980f5362fc7bf56d3341d183aa9b13fd/README.yaml index 5a50771b52..e55cd4c91e 100644 --- a/Simulations/d34/73d/d3473d6d3560f722e43a5715b8eafba1192e809f/5e83fee5980f5362fc7bf56d3341d183aa9b13fd/README.yaml +++ b/Simulations/d34/73d/d3473d6d3560f722e43a5715b8eafba1192e809f/5e83fee5980f5362fc7bf56d3341d183aa9b13fd/README.yaml @@ -40,9 +40,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 227 bioschema_properties: - name: Molecular dynamics trajectory of a DPPE bilayer at 336 K (Slipids, GROMACS 5.0.4, 50 ns) [NMRlipids simulation 227] + name: Molecular dynamics trajectory of a DPPE bilayer at 336 K (Slipids, GROMACS + 5.0.4, 50 ns) [NMRlipids simulation 227] alternateName: 288DPPE_9386SOL_336K - description: Molecular dynamics trajectory of a lipid bilayer of 288 DPPE (1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine) at 336 K. Simulated with Slipids in GROMACS 5.0.4 for 50 ns (63006 atoms). Deposited as NMRlipids Databank simulation 227 and available from https://doi.org/10.5281/zenodo.495247. + description: Molecular dynamics trajectory of a lipid bilayer of 288 DPPE (1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine) + at 336 K. Simulated with Slipids in GROMACS 5.0.4 for 50 ns (63006 atoms). Deposited + as NMRlipids Databank simulation 227 and available from https://doi.org/10.5281/zenodo.495247. sameAs: https://doi.org/10.5281/zenodo.495247 datePublished: '2017-04-06' license: @@ -129,7 +132,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.495247 identifier: 10.5281/zenodo.495247 url: https://doi.org/10.5281/zenodo.495247 - name: 'Md Simulation Trajectory Of A Fully Hydrated Dppe Bilayer: Slipids, Gromacs 5.0.4. 2017.' + name: 'Md Simulation Trajectory Of A Fully Hydrated Dppe Bilayer: Slipids, Gromacs + 5.0.4. 2017.' publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/d38/489/d384893b2e7f68d4d0319041624dc3470e8fa09f/6736d2b6f7e8ebc2e92048646a3afa535f1a529d/README.yaml b/Simulations/d38/489/d384893b2e7f68d4d0319041624dc3470e8fa09f/6736d2b6f7e8ebc2e92048646a3afa535f1a529d/README.yaml index 366784662f..0e191d8d4d 100644 --- a/Simulations/d38/489/d384893b2e7f68d4d0319041624dc3470e8fa09f/6736d2b6f7e8ebc2e92048646a3afa535f1a529d/README.yaml +++ b/Simulations/d38/489/d384893b2e7f68d4d0319041624dc3470e8fa09f/6736d2b6f7e8ebc2e92048646a3afa535f1a529d/README.yaml @@ -33,9 +33,12 @@ EXPERIMENT: DPPC: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a DPPC bilayer at 333 K (SLIPIDS, GROMACS, 100 ns) [NMRlipids simulation 898] + name: Molecular dynamics trajectory of a DPPC bilayer at 333 K (SLIPIDS, GROMACS, + 100 ns) [NMRlipids simulation 898] alternateName: DPPC - description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) at 333 K. Simulated with SLIPIDS in GROMACS for 100 ns (13347 atoms). Deposited as NMRlipids Databank simulation 898 and available from https://doi.org/10.5281/zenodo.7572990. + description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) + at 333 K. Simulated with SLIPIDS in GROMACS for 100 ns (13347 atoms). Deposited + as NMRlipids Databank simulation 898 and available from https://doi.org/10.5281/zenodo.7572990. sameAs: https://doi.org/10.5281/zenodo.7572990 datePublished: '2023-01-26' license: @@ -125,7 +128,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.7572990 identifier: 10.5281/zenodo.7572990 url: https://doi.org/10.5281/zenodo.7572990 - name: 'MD simulation input files and results for ,,Atomistic MD simulations of n-alkanes in a phospholipid bilayer: CHARMM36 versus Slipids"' + name: 'MD simulation input files and results for ,,Atomistic MD simulations of + n-alkanes in a phospholipid bilayer: CHARMM36 versus Slipids"' publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/d38/af3/d38af3e2db58923349c47aa672f819290f221094/d38af3e2db58923349c47aa672f819290f221094/README.yaml b/Simulations/d38/af3/d38af3e2db58923349c47aa672f819290f221094/d38af3e2db58923349c47aa672f819290f221094/README.yaml index fdb60fa795..bd4625ad67 100644 --- a/Simulations/d38/af3/d38af3e2db58923349c47aa672f819290f221094/d38af3e2db58923349c47aa672f819290f221094/README.yaml +++ b/Simulations/d38/af3/d38af3e2db58923349c47aa672f819290f221094/d38af3e2db58923349c47aa672f819290f221094/README.yaml @@ -38,9 +38,12 @@ EXPERIMENT: FORMFACTOR: - 10.1016/j.chemphyslip.2020.104892/1 bioschema_properties: - name: Molecular dynamics trajectory of a PDPC bilayer at 303.15 K (CHARMM36m, NAMD 3, 500 ns) [NMRlipids simulation 903] + name: Molecular dynamics trajectory of a PDPC bilayer at 303.15 K (CHARMM36m, NAMD + 3, 500 ns) [NMRlipids simulation 903] alternateName: PDPC - description: Molecular dynamics trajectory of a lipid bilayer of 200 PDPC (1-palmitoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine) at 303.15 K. Simulated with CHARMM36m in NAMD 3 for 500 ns (54200 atoms). Deposited as NMRlipids Databank simulation 903 and available from https://doi.org/10.5281/zenodo.18471696. + description: Molecular dynamics trajectory of a lipid bilayer of 200 PDPC (1-palmitoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine) + at 303.15 K. Simulated with CHARMM36m in NAMD 3 for 500 ns (54200 atoms). Deposited + as NMRlipids Databank simulation 903 and available from https://doi.org/10.5281/zenodo.18471696. sameAs: https://doi.org/10.5281/zenodo.18471696 datePublished: '2026-02-03' license: @@ -131,7 +134,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.18471696 identifier: 10.5281/zenodo.18471696 url: https://doi.org/10.5281/zenodo.18471696 - name: 1-palmitoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine (PDPC) lipid bilayer , 303K, CHARMM36m-WYF forcefield, NAMD 3.0.2, 2* 500 ns + name: 1-palmitoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine (PDPC) lipid bilayer + , 303K, CHARMM36m-WYF forcefield, NAMD 3.0.2, 2* 500 ns publisher: Zenodo _source: api: datacite diff --git a/Simulations/d3b/a29/d3ba29f12ba3af0c6e1f58f0884c9365040f796f/355bb07458737ad70f0ff5f128fea71521b58f58/README.yaml b/Simulations/d3b/a29/d3ba29f12ba3af0c6e1f58f0884c9365040f796f/355bb07458737ad70f0ff5f128fea71521b58f58/README.yaml index 9117d1cb6a..efde9bd243 100644 --- a/Simulations/d3b/a29/d3ba29f12ba3af0c6e1f58f0884c9365040f796f/355bb07458737ad70f0ff5f128fea71521b58f58/README.yaml +++ b/Simulations/d3b/a29/d3ba29f12ba3af0c6e1f58f0884c9365040f796f/355bb07458737ad70f0ff5f128fea71521b58f58/README.yaml @@ -55,9 +55,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 20 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/CLA/SOD (41:29:29) bilayer at 323 K (OPLSAA-compatible Berger-DPPC-06, GROMACS 5.0.4, 120 ns) [NMRlipids simulation 20] + name: Molecular dynamics trajectory of a DPPC/CLA/SOD (41:29:29) bilayer at 323 + K (OPLSAA-compatible Berger-DPPC-06, GROMACS 5.0.4, 120 ns) [NMRlipids simulation + 20] alternateName: 72DPPC_2778SOL_51SOD_51CLA_323K - description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 41 mol%), 51 CLA (29 mol%) and 51 SOD (29 mol%) at 323 K. Simulated with OPLSAA-compatible Berger-DPPC-06 in GROMACS 5.0.4 for 120 ns (12036 atoms). Deposited as NMRlipids Databank simulation 20 and available from https://doi.org/10.5281/zenodo.46152. + description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 41 mol%), 51 CLA (29 mol%) and 51 SOD (29 mol%) at 323 K. Simulated with OPLSAA-compatible + Berger-DPPC-06 in GROMACS 5.0.4 for 120 ns (12036 atoms). Deposited as NMRlipids + Databank simulation 20 and available from https://doi.org/10.5281/zenodo.46152. sameAs: https://doi.org/10.5281/zenodo.46152 datePublished: '2016-02-17' license: diff --git a/Simulations/d3e/243/d3e243f27cb9f0e5ffaf9b52755273086407bb44/d3e243f27cb9f0e5ffaf9b52755273086407bb44/README.yaml b/Simulations/d3e/243/d3e243f27cb9f0e5ffaf9b52755273086407bb44/d3e243f27cb9f0e5ffaf9b52755273086407bb44/README.yaml index c7ad42a51e..a01f6a0fa9 100644 --- a/Simulations/d3e/243/d3e243f27cb9f0e5ffaf9b52755273086407bb44/d3e243f27cb9f0e5ffaf9b52755273086407bb44/README.yaml +++ b/Simulations/d3e/243/d3e243f27cb9f0e5ffaf9b52755273086407bb44/d3e243f27cb9f0e5ffaf9b52755273086407bb44/README.yaml @@ -59,9 +59,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 922 bioschema_properties: - name: Molecular dynamics trajectory of a CHOL/POPC/SM18/CLA/SOD (28:28:28:8:8) bilayer at 303.15 K (Charmm36, NAMD NAMD 2.13, 0 ns) [NMRlipids simulation 922] + name: Molecular dynamics trajectory of a CHOL/POPC/SM18/CLA/SOD (28:28:28:8:8) bilayer + at 303.15 K (Charmm36, NAMD NAMD 2.13, 0 ns) [NMRlipids simulation 922] alternateName: POPC:SSM(sphingomyelin):CHOL(1:1:1) - description: Molecular dynamics trajectory of a lipid bilayer of 276 CHOL (cholesterol, 28 mol%), 276 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 28 mol%), 276 SM18 (N-stearoyl-D-erythro-sphingosylphosphorylcholine, 28 mol%), 77 CLA (8 mol%) and 77 SOD (8 mol%) at 303.15 K. Simulated with Charmm36 in NAMD NAMD 2.13 for 0 ns (181519 atoms). Deposited as NMRlipids Databank simulation 922 and available from https://doi.org/10.5281/zenodo.21937938. + description: Molecular dynamics trajectory of a lipid bilayer of 276 CHOL (cholesterol, + 28 mol%), 276 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 28 mol%), + 276 SM18 (N-stearoyl-D-erythro-sphingosylphosphorylcholine, 28 mol%), 77 CLA (8 + mol%) and 77 SOD (8 mol%) at 303.15 K. Simulated with Charmm36 in NAMD NAMD 2.13 + for 0 ns (181519 atoms). Deposited as NMRlipids Databank simulation 922 and available + from https://doi.org/10.5281/zenodo.21937938. sameAs: https://doi.org/10.5281/zenodo.21937938 datePublished: '2026-08-14' license: @@ -164,4 +170,4 @@ bioschema_properties: api: datacite doi: 10.5281/zenodo.21937938 spdxLicenseList: 3.28.0 - retrieved: '2026-09-09' \ No newline at end of file + retrieved: '2026-09-09' diff --git a/Simulations/d41/0a0/d410a0c257276ccda5fcc3b444ee87e7a41cc940/38ede40be484a826ca8af53369965277ebe29e43/README.yaml b/Simulations/d41/0a0/d410a0c257276ccda5fcc3b444ee87e7a41cc940/38ede40be484a826ca8af53369965277ebe29e43/README.yaml index 30ddf8daf8..d351c62ee2 100644 --- a/Simulations/d41/0a0/d410a0c257276ccda5fcc3b444ee87e7a41cc940/38ede40be484a826ca8af53369965277ebe29e43/README.yaml +++ b/Simulations/d41/0a0/d410a0c257276ccda5fcc3b444ee87e7a41cc940/38ede40be484a826ca8af53369965277ebe29e43/README.yaml @@ -39,3 +39,7 @@ NUMBER_OF_ATOMS: 53000 DATEOFRUNNING: 15/09/2026 TYPEOFSYSTEM: lipid bilayer ID: 930 +EXPERIMENT: + ORDERPARAMETER: + DPPC: [] + FORMFACTOR: [] diff --git a/Simulations/d44/b08/d44b08236b42139f46a3fbbbd840e239070fb0b8/60bc71c1212d826e4842a448c90cbd8506142e69/README.yaml b/Simulations/d44/b08/d44b08236b42139f46a3fbbbd840e239070fb0b8/60bc71c1212d826e4842a448c90cbd8506142e69/README.yaml index d11904f622..9b2b60db58 100644 --- a/Simulations/d44/b08/d44b08236b42139f46a3fbbbd840e239070fb0b8/60bc71c1212d826e4842a448c90cbd8506142e69/README.yaml +++ b/Simulations/d44/b08/d44b08236b42139f46a3fbbbd840e239070fb0b8/60bc71c1212d826e4842a448c90cbd8506142e69/README.yaml @@ -41,9 +41,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 455 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC bilayer at 288 K (CHARMM36, GROMACS 2016.4, 50 ns) [NMRlipids simulation 455] + name: Molecular dynamics trajectory of a DPPC bilayer at 288 K (CHARMM36, GROMACS + 2016.4, 50 ns) [NMRlipids simulation 455] alternateName: 64DPPC_10623SOL_288K - description: Molecular dynamics trajectory of a lipid bilayer of 64 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) at 288 K. Simulated with CHARMM36 in GROMACS 2016.4 for 50 ns (40189 atoms). Deposited as NMRlipids Databank simulation 455 and available from https://doi.org/10.5281/zenodo.4522359. + description: Molecular dynamics trajectory of a lipid bilayer of 64 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) + at 288 K. Simulated with CHARMM36 in GROMACS 2016.4 for 50 ns (40189 atoms). Deposited + as NMRlipids Databank simulation 455 and available from https://doi.org/10.5281/zenodo.4522359. sameAs: https://doi.org/10.5281/zenodo.4522359 datePublished: '2021-02-09' license: diff --git a/Simulations/d45/b05/d45b05bc99386840c573e3d7267667afe16526fe/720a899e06ba483b86b0158f41ec691559f72939/README.yaml b/Simulations/d45/b05/d45b05bc99386840c573e3d7267667afe16526fe/720a899e06ba483b86b0158f41ec691559f72939/README.yaml index 8cf1b1fa47..00dd1d0d77 100644 --- a/Simulations/d45/b05/d45b05bc99386840c573e3d7267667afe16526fe/720a899e06ba483b86b0158f41ec691559f72939/README.yaml +++ b/Simulations/d45/b05/d45b05bc99386840c573e3d7267667afe16526fe/720a899e06ba483b86b0158f41ec691559f72939/README.yaml @@ -43,9 +43,12 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 320 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 310.15 K (CHARMM36, GROMACS 5, 734 ns) [NMRlipids simulation 320] + name: Molecular dynamics trajectory of a POPC bilayer at 310.15 K (CHARMM36, GROMACS + 5, 734 ns) [NMRlipids simulation 320] alternateName: 200POPC_10456SOL_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 310.15 K. Simulated with CHARMM36 in GROMACS 5 for 734 ns (68624 atoms). Deposited as NMRlipids Databank simulation 320 and available from https://doi.org/10.5281/zenodo.3431948. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 310.15 K. Simulated with CHARMM36 in GROMACS 5 for 734 ns (68624 atoms). Deposited + as NMRlipids Databank simulation 320 and available from https://doi.org/10.5281/zenodo.3431948. sameAs: https://doi.org/10.5281/zenodo.3431948 datePublished: '2019-09-17' license: diff --git a/Simulations/d49/d48/d49d482e7e37b1934cd7a67f9689aba95d13f437/d8957bcc992e9925a9532d54fb8b8100daf6c9b1/README.yaml b/Simulations/d49/d48/d49d482e7e37b1934cd7a67f9689aba95d13f437/d8957bcc992e9925a9532d54fb8b8100daf6c9b1/README.yaml index 9f7380d1f8..53b7b59483 100644 --- a/Simulations/d49/d48/d49d482e7e37b1934cd7a67f9689aba95d13f437/d8957bcc992e9925a9532d54fb8b8100daf6c9b1/README.yaml +++ b/Simulations/d49/d48/d49d482e7e37b1934cd7a67f9689aba95d13f437/d8957bcc992e9925a9532d54fb8b8100daf6c9b1/README.yaml @@ -49,9 +49,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 615 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (60:40) bilayer at 310 K (CHARMM36, GROMACS, 500 ns) [NMRlipids simulation 615] + name: Molecular dynamics trajectory of a POPC/CHOL (60:40) bilayer at 310 K (CHARMM36, + GROMACS, 500 ns) [NMRlipids simulation 615] alternateName: 134CHOL_200POPC_15030SOL_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 60 mol%) and 134 CHOL (cholesterol, 40 mol%) at 310 K. Simulated with CHARMM36 in GROMACS for 500 ns (81806 atoms). Deposited as NMRlipids Databank simulation 615 and available from https://doi.org/10.5281/zenodo.3238157. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 60 mol%) and 134 CHOL (cholesterol, 40 mol%) at 310 K. Simulated with CHARMM36 + in GROMACS for 500 ns (81806 atoms). Deposited as NMRlipids Databank simulation + 615 and available from https://doi.org/10.5281/zenodo.3238157. sameAs: https://doi.org/10.5281/zenodo.3238157 datePublished: '2016-09-08' license: diff --git a/Simulations/d56/3fc/d563fceec21a92d5469126f291c0a69984e58ede/050697557b5116b6faceef3b80c2178a6f44d7ae/README.yaml b/Simulations/d56/3fc/d563fceec21a92d5469126f291c0a69984e58ede/050697557b5116b6faceef3b80c2178a6f44d7ae/README.yaml index e9270c86f8..9edea8a781 100644 --- a/Simulations/d56/3fc/d563fceec21a92d5469126f291c0a69984e58ede/050697557b5116b6faceef3b80c2178a6f44d7ae/README.yaml +++ b/Simulations/d56/3fc/d563fceec21a92d5469126f291c0a69984e58ede/050697557b5116b6faceef3b80c2178a6f44d7ae/README.yaml @@ -56,9 +56,14 @@ EXPERIMENT: SM16: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a POPC/SM16/CHOL (35:35:30) bilayer at 295 K (Slipids, GROMACS 5.1.4, 100 ns) [NMRlipids simulation 849] + name: Molecular dynamics trajectory of a POPC/SM16/CHOL (35:35:30) bilayer at 295 + K (Slipids, GROMACS 5.1.4, 100 ns) [NMRlipids simulation 849] alternateName: POPC/SM16/CHOL (35:35:30) - description: Molecular dynamics trajectory of a lipid bilayer of 360 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 35 mol%), 352 SM16 (N-palmitoyl-D-erythro-sphingosylphosphorylcholine, 35 mol%) and 304 CHOL (cholesterol, 30 mol%) at 295 K. Simulated with Slipids in GROMACS 5.1.4 for 100 ns (222960 atoms). Deposited as NMRlipids Databank simulation 849 and available from https://doi.org/10.5281/zenodo.17730864. + description: Molecular dynamics trajectory of a lipid bilayer of 360 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 35 mol%), 352 SM16 (N-palmitoyl-D-erythro-sphingosylphosphorylcholine, 35 mol%) + and 304 CHOL (cholesterol, 30 mol%) at 295 K. Simulated with Slipids in GROMACS + 5.1.4 for 100 ns (222960 atoms). Deposited as NMRlipids Databank simulation 849 + and available from https://doi.org/10.5281/zenodo.17730864. sameAs: https://doi.org/10.5281/zenodo.17730864 datePublished: '2025-11-27' license: @@ -154,7 +159,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.17730864 identifier: 10.5281/zenodo.17730864 url: https://doi.org/10.5281/zenodo.17730864 - name: 'MD simulation trajectory of Ternary mixture of POPC/PSM/Chol (35:35:30) at 295 K: Slipids, GROMACS 5.1.4.' + name: 'MD simulation trajectory of Ternary mixture of POPC/PSM/Chol (35:35:30) + at 295 K: Slipids, GROMACS 5.1.4.' publisher: Zenodo _source: api: datacite diff --git a/Simulations/d56/af7/d56af76f2bc3c77ecb6b255dd1e6e4a304621a22/98cde4f05842054793d2430b174329e176982042/README.yaml b/Simulations/d56/af7/d56af76f2bc3c77ecb6b255dd1e6e4a304621a22/98cde4f05842054793d2430b174329e176982042/README.yaml index e820987729..b443a00f3c 100644 --- a/Simulations/d56/af7/d56af76f2bc3c77ecb6b255dd1e6e4a304621a22/98cde4f05842054793d2430b174329e176982042/README.yaml +++ b/Simulations/d56/af7/d56af76f2bc3c77ecb6b255dd1e6e4a304621a22/98cde4f05842054793d2430b174329e176982042/README.yaml @@ -50,9 +50,13 @@ WARNINGS: PBC: z-jumps ID: 421 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (66:34) bilayer at 303 K (Lipid14, GROMACS 5.0.4, 200 ns) [NMRlipids simulation 421] + name: Molecular dynamics trajectory of a POPC/CHOL (66:34) bilayer at 303 K (Lipid14, + GROMACS 5.0.4, 200 ns) [NMRlipids simulation 421] alternateName: 84POPC_44CHOL_3968SOL_303K - description: Molecular dynamics trajectory of a lipid bilayer of 84 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 66 mol%) and 44 CHOL (cholesterol, 34 mol%) at 303 K. Simulated with Lipid14 in GROMACS 5.0.4 for 200 ns (26416 atoms). Deposited as NMRlipids Databank simulation 421 and available from https://doi.org/10.5281/zenodo.3871004. + description: Molecular dynamics trajectory of a lipid bilayer of 84 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 66 mol%) and 44 CHOL (cholesterol, 34 mol%) at 303 K. Simulated with Lipid14 in + GROMACS 5.0.4 for 200 ns (26416 atoms). Deposited as NMRlipids Databank simulation + 421 and available from https://doi.org/10.5281/zenodo.3871004. sameAs: https://doi.org/10.5281/zenodo.3871004 datePublished: '2020-06-01' license: @@ -141,7 +145,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3871004 identifier: 10.5281/zenodo.3871004 url: https://doi.org/10.5281/zenodo.3871004 - name: 'MD simulations of bilayers containing POPC and Cholesterol: 84POPC_44CHL_31Nwat_neutral (lipid14)' + name: 'MD simulations of bilayers containing POPC and Cholesterol: 84POPC_44CHL_31Nwat_neutral + (lipid14)' publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/d6d/09c/d6d09c4458210fdf02a4be6b84e90f2ccb3cd878/7d2df313040867886d85e66f378f5689d6505517/README.yaml b/Simulations/d6d/09c/d6d09c4458210fdf02a4be6b84e90f2ccb3cd878/7d2df313040867886d85e66f378f5689d6505517/README.yaml index 6540c2bd9d..c7323d11ee 100644 --- a/Simulations/d6d/09c/d6d09c4458210fdf02a4be6b84e90f2ccb3cd878/7d2df313040867886d85e66f378f5689d6505517/README.yaml +++ b/Simulations/d6d/09c/d6d09c4458210fdf02a4be6b84e90f2ccb3cd878/7d2df313040867886d85e66f378f5689d6505517/README.yaml @@ -44,9 +44,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 203 bioschema_properties: - name: Molecular dynamics trajectory of a POPS/POT (50:50) bilayer at 298 K (CHARMM36, GROMACS, 100 ns) [NMRlipids simulation 203] + name: Molecular dynamics trajectory of a POPS/POT (50:50) bilayer at 298 K (CHARMM36, + GROMACS, 100 ns) [NMRlipids simulation 203] alternateName: 128POPS_128POT_4480SOL_298K_v2 - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 50 mol%) and 128 POT (50 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for 100 ns (29824 atoms). Deposited as NMRlipids Databank simulation 203 and available from https://doi.org/10.5281/zenodo.1182654. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, + 50 mol%) and 128 POT (50 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for + 100 ns (29824 atoms). Deposited as NMRlipids Databank simulation 203 and available + from https://doi.org/10.5281/zenodo.1182654. sameAs: https://doi.org/10.5281/zenodo.1182654 datePublished: '2018-02-21' license: @@ -132,7 +136,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1182654 identifier: 10.5281/zenodo.1182654 url: https://doi.org/10.5281/zenodo.1182654 - name: Charmm36 Pops Simulations (Versions 1 And 2) 298 K 1.0 Nm Lj Switching With K Ions + name: Charmm36 Pops Simulations (Versions 1 And 2) 298 K 1.0 Nm Lj Switching With + K Ions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/d6e/876/d6e8760c898e670bf6a7dc97bca1c447a14bea86/9623c65208f06e641776ae88baf08feda0d09f16/README.yaml b/Simulations/d6e/876/d6e8760c898e670bf6a7dc97bca1c447a14bea86/9623c65208f06e641776ae88baf08feda0d09f16/README.yaml index 2b0e436e1c..953cc28b7f 100644 --- a/Simulations/d6e/876/d6e8760c898e670bf6a7dc97bca1c447a14bea86/9623c65208f06e641776ae88baf08feda0d09f16/README.yaml +++ b/Simulations/d6e/876/d6e8760c898e670bf6a7dc97bca1c447a14bea86/9623c65208f06e641776ae88baf08feda0d09f16/README.yaml @@ -55,9 +55,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 527 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (52:32:16) bilayer at 313 K (ECC-lipids, GROMACS 5.1.4, 300 ns) [NMRlipids simulation 527] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (52:32:16) bilayer at 313 + K (ECC-lipids, GROMACS 5.1.4, 300 ns) [NMRlipids simulation 527] alternateName: 128POPC_6400SOL_40CAL_80CLA_313K_OPC3model - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 52 mol%), 80 CLA (32 mol%) and 40 CAL (16 mol%) at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 300 ns (36472 atoms). Deposited as NMRlipids Databank simulation 527 and available from https://doi.org/10.5281/zenodo.1118980. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 52 mol%), 80 CLA (32 mol%) and 40 CAL (16 mol%) at 313 K. Simulated with ECC-lipids + in GROMACS 5.1.4 for 300 ns (36472 atoms). Deposited as NMRlipids Databank simulation + 527 and available from https://doi.org/10.5281/zenodo.1118980. sameAs: https://doi.org/10.5281/zenodo.1118980 datePublished: '2017-12-19' license: @@ -147,7 +151,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1118980 identifier: 10.5281/zenodo.1118980 url: https://doi.org/10.5281/zenodo.1118980 - name: Simulations Of Popc Lipid Bilayer In Water Solution At Various Nacl And Cacl2 Concentrations Using Ecc-Popc Force Field And Various Water Models + name: Simulations Of Popc Lipid Bilayer In Water Solution At Various Nacl And + Cacl2 Concentrations Using Ecc-Popc Force Field And Various Water Models publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/d6f/8da/d6f8dac94d5efed0f3a7fd74534c04d06f26cfdb/e8f7849bc0bf087c8b9179fb8d37fec6fc6e184d/README.yaml b/Simulations/d6f/8da/d6f8dac94d5efed0f3a7fd74534c04d06f26cfdb/e8f7849bc0bf087c8b9179fb8d37fec6fc6e184d/README.yaml index 794c4acaa6..340a05922c 100644 --- a/Simulations/d6f/8da/d6f8dac94d5efed0f3a7fd74534c04d06f26cfdb/e8f7849bc0bf087c8b9179fb8d37fec6fc6e184d/README.yaml +++ b/Simulations/d6f/8da/d6f8dac94d5efed0f3a7fd74534c04d06f26cfdb/e8f7849bc0bf087c8b9179fb8d37fec6fc6e184d/README.yaml @@ -48,9 +48,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 479 bioschema_properties: - name: Molecular dynamics trajectory of a DOPS/SOD (50:50) bilayer at 303 K (CHARMM36-UA, GROMACS, 100 ns) [NMRlipids simulation 479] + name: Molecular dynamics trajectory of a DOPS/SOD (50:50) bilayer at 303 K (CHARMM36-UA, + GROMACS, 100 ns) [NMRlipids simulation 479] alternateName: 128DOPS_4480SOL_128SOD_303K_v1 - description: Molecular dynamics trajectory of a lipid bilayer of 128 DOPS (1,2-dioleoyl-sn-glycero-3-phospho-L-serine, 50 mol%) and 128 SOD (50 mol%) at 303 K. Simulated with CHARMM36-UA in GROMACS for 100 ns (22400 atoms). Deposited as NMRlipids Databank simulation 479 and available from https://doi.org/10.5281/zenodo.1129456. + description: Molecular dynamics trajectory of a lipid bilayer of 128 DOPS (1,2-dioleoyl-sn-glycero-3-phospho-L-serine, + 50 mol%) and 128 SOD (50 mol%) at 303 K. Simulated with CHARMM36-UA in GROMACS + for 100 ns (22400 atoms). Deposited as NMRlipids Databank simulation 479 and available + from https://doi.org/10.5281/zenodo.1129456. sameAs: https://doi.org/10.5281/zenodo.1129456 datePublished: '2017-12-24' license: diff --git a/Simulations/d70/794/d707941fbaef0056a64c36538463439b819fd56c/d694776374b43a9cdc05923d515bd47898c12f4e/README.yaml b/Simulations/d70/794/d707941fbaef0056a64c36538463439b819fd56c/d694776374b43a9cdc05923d515bd47898c12f4e/README.yaml index 5b5ac8de78..8064836723 100644 --- a/Simulations/d70/794/d707941fbaef0056a64c36538463439b819fd56c/d694776374b43a9cdc05923d515bd47898c12f4e/README.yaml +++ b/Simulations/d70/794/d707941fbaef0056a64c36538463439b819fd56c/d694776374b43a9cdc05923d515bd47898c12f4e/README.yaml @@ -50,9 +50,13 @@ SOFTWARE: gromacs DIR_WRK: /usr/home/bort/Databank ID: 493 bioschema_properties: - name: Molecular dynamics trajectory of a DAPC/CHOL (90:10) bilayer at 333 K (CHARMM36, GROMACS, 1000 ns) [NMRlipids simulation 493] + name: Molecular dynamics trajectory of a DAPC/CHOL (90:10) bilayer at 333 K (CHARMM36, + GROMACS, 1000 ns) [NMRlipids simulation 493] alternateName: 260DAPC_28CHOL_11520SOL_333K - description: Molecular dynamics trajectory of a lipid bilayer of 260 DAPC (1,2-diarachidonoyl-sn-glycero-3-phosphocholine, 90 mol%) and 28 CHOL (cholesterol, 10 mol%) at 333 K. Simulated with CHARMM36 in GROMACS for 1000 ns (72512 atoms). Deposited as NMRlipids Databank simulation 493 and available from https://doi.org/10.5281/zenodo.2653721. + description: Molecular dynamics trajectory of a lipid bilayer of 260 DAPC (1,2-diarachidonoyl-sn-glycero-3-phosphocholine, + 90 mol%) and 28 CHOL (cholesterol, 10 mol%) at 333 K. Simulated with CHARMM36 + in GROMACS for 1000 ns (72512 atoms). Deposited as NMRlipids Databank simulation + 493 and available from https://doi.org/10.5281/zenodo.2653721. sameAs: https://doi.org/10.5281/zenodo.2653721 datePublished: '2019-04-29' license: @@ -141,7 +145,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.2653721 identifier: 10.5281/zenodo.2653721 url: https://doi.org/10.5281/zenodo.2653721 - name: Atomistic simulations of cholesterol in symmetric lipid bilayers with varying degrees of lipid chain unsaturation + name: Atomistic simulations of cholesterol in symmetric lipid bilayers with varying + degrees of lipid chain unsaturation publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/d75/98d/d7598d086c88dc124680de8cb44dd99110d85036/702ce2db902f3fb85b89677b0da2444daff0eea8/README.yaml b/Simulations/d75/98d/d7598d086c88dc124680de8cb44dd99110d85036/702ce2db902f3fb85b89677b0da2444daff0eea8/README.yaml index fc8240f6d4..31c248bc73 100644 --- a/Simulations/d75/98d/d7598d086c88dc124680de8cb44dd99110d85036/702ce2db902f3fb85b89677b0da2444daff0eea8/README.yaml +++ b/Simulations/d75/98d/d7598d086c88dc124680de8cb44dd99110d85036/702ce2db902f3fb85b89677b0da2444daff0eea8/README.yaml @@ -55,9 +55,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 524 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPS/SOD (33:33:33) bilayer at 298 K (Lipid17 and Dang ions, GROMACS 2018.0, 1000 ns) [NMRlipids simulation 524] + name: Molecular dynamics trajectory of a POPC/POPS/SOD (33:33:33) bilayer at 298 + K (Lipid17 and Dang ions, GROMACS 2018.0, 1000 ns) [NMRlipids simulation 524] alternateName: 64POPC_64POPS_5253SOL_64SOD_298K - description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 33 mol%), 64 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 33 mol%) and 64 SOD (33 mol%) at 298 K. Simulated with Lipid17 and Dang ions in GROMACS 2018.0 for 1000 ns (32527 atoms). Deposited as NMRlipids Databank simulation 524 and available from https://doi.org/10.5281/zenodo.1487761. + description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 33 mol%), 64 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 33 mol%) + and 64 SOD (33 mol%) at 298 K. Simulated with Lipid17 and Dang ions in GROMACS + 2018.0 for 1000 ns (32527 atoms). Deposited as NMRlipids Databank simulation 524 + and available from https://doi.org/10.5281/zenodo.1487761. sameAs: https://doi.org/10.5281/zenodo.1487761 datePublished: '2018-11-14' license: @@ -148,7 +153,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1487761 identifier: 10.5281/zenodo.1487761 url: https://doi.org/10.5281/zenodo.1487761 - name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS with the lipid17 force field, only counterions, and CaCl2 concentrations + name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS + with the lipid17 force field, only counterions, and CaCl2 concentrations publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/d7d/10b/d7d10b044a4dca1837d9aed145f288a1549073f7/235d29651e1726b997a486036fecc6dec41f60e3/README.yaml b/Simulations/d7d/10b/d7d10b044a4dca1837d9aed145f288a1549073f7/235d29651e1726b997a486036fecc6dec41f60e3/README.yaml index a19d41ca4b..ed92a52d86 100644 --- a/Simulations/d7d/10b/d7d10b044a4dca1837d9aed145f288a1549073f7/235d29651e1726b997a486036fecc6dec41f60e3/README.yaml +++ b/Simulations/d7d/10b/d7d10b044a4dca1837d9aed145f288a1549073f7/235d29651e1726b997a486036fecc6dec41f60e3/README.yaml @@ -50,9 +50,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 346 bioschema_properties: - name: Molecular dynamics trajectory of a DOPC/CLA/SOD (83:9:9) bilayer at 310 K (Slipids for lipids and Smith & Dang for ions, GROMACS 4.6, 200 ns) [NMRlipids simulation 346] + name: Molecular dynamics trajectory of a DOPC/CLA/SOD (83:9:9) bilayer at 310 K + (Slipids for lipids and Smith & Dang for ions, GROMACS 4.6, 200 ns) [NMRlipids + simulation 346] alternateName: 200DOPC_9000SOL_21SOD_21CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, 83 mol%), 21 CLA (9 mol%) and 21 SOD (9 mol%) at 310 K. Simulated with Slipids for lipids and Smith & Dang for ions in GROMACS 4.6 for 200 ns (54642 atoms). Deposited as NMRlipids Databank simulation 346 and available from https://doi.org/10.5281/zenodo.259443. + description: Molecular dynamics trajectory of a lipid bilayer of 200 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, + 83 mol%), 21 CLA (9 mol%) and 21 SOD (9 mol%) at 310 K. Simulated with Slipids + for lipids and Smith & Dang for ions in GROMACS 4.6 for 200 ns (54642 atoms). + Deposited as NMRlipids Databank simulation 346 and available from https://doi.org/10.5281/zenodo.259443. sameAs: https://doi.org/10.5281/zenodo.259443 datePublished: '2017-01-24' license: diff --git a/Simulations/d7d/a77/d7da777e58b34af38c76dc023857c293d969a727/95b02b37db5834c23ea58f2e57ab259fb627934e/README.yaml b/Simulations/d7d/a77/d7da777e58b34af38c76dc023857c293d969a727/95b02b37db5834c23ea58f2e57ab259fb627934e/README.yaml index 9dfbe8e07f..e71e3058db 100644 --- a/Simulations/d7d/a77/d7da777e58b34af38c76dc023857c293d969a727/95b02b37db5834c23ea58f2e57ab259fb627934e/README.yaml +++ b/Simulations/d7d/a77/d7da777e58b34af38c76dc023857c293d969a727/95b02b37db5834c23ea58f2e57ab259fb627934e/README.yaml @@ -61,9 +61,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 348 bioschema_properties: - name: Molecular dynamics trajectory of a POPE/SOD/POPG/CLA (52:24:17:7) bilayer at 310 K (GROMOS-CKP, GROMACS 5.1.2, 100 ns) [NMRlipids simulation 348] + name: Molecular dynamics trajectory of a POPE/SOD/POPG/CLA (52:24:17:7) bilayer + at 310 K (GROMOS-CKP, GROMACS 5.1.2, 100 ns) [NMRlipids simulation 348] alternateName: 126POPG_374POPE_25000SOL_176SOD_50CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 374 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 52 mol%), 176 SOD (24 mol%), 126 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 17 mol%) and 50 CLA (7 mol%) at 310 K. Simulated with GROMOS-CKP in GROMACS 5.1.2 for 100 ns (101352 atoms). Deposited as NMRlipids Databank simulation 348 and available from https://doi.org/10.5281/zenodo.2579063. + description: Molecular dynamics trajectory of a lipid bilayer of 374 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, + 52 mol%), 176 SOD (24 mol%), 126 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, + 17 mol%) and 50 CLA (7 mol%) at 310 K. Simulated with GROMOS-CKP in GROMACS 5.1.2 + for 100 ns (101352 atoms). Deposited as NMRlipids Databank simulation 348 and + available from https://doi.org/10.5281/zenodo.2579063. sameAs: https://doi.org/10.5281/zenodo.2579063 datePublished: '2019-02-27' license: @@ -156,7 +161,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.2579063 identifier: 10.5281/zenodo.2579063 url: https://doi.org/10.5281/zenodo.2579063 - name: GOMOS-CKP POPG-POPE 1:3 Bilayer Simulation (Last 100 ns, 150 mM NaCl, 310 K ) + name: GOMOS-CKP POPG-POPE 1:3 Bilayer Simulation (Last 100 ns, 150 mM NaCl, 310 + K ) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/d7d/e4e/d7de4eb98126d515bf4b05457472d8d980c6ab2a/9245e3215d0b86b8fc83ef6b7ecff10c113dc50e/README.yaml b/Simulations/d7d/e4e/d7de4eb98126d515bf4b05457472d8d980c6ab2a/9245e3215d0b86b8fc83ef6b7ecff10c113dc50e/README.yaml index 6b746700dc..331cd51e41 100644 --- a/Simulations/d7d/e4e/d7de4eb98126d515bf4b05457472d8d980c6ab2a/9245e3215d0b86b8fc83ef6b7ecff10c113dc50e/README.yaml +++ b/Simulations/d7d/e4e/d7de4eb98126d515bf4b05457472d8d980c6ab2a/9245e3215d0b86b8fc83ef6b7ecff10c113dc50e/README.yaml @@ -55,9 +55,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 347 bioschema_properties: - name: Molecular dynamics trajectory of a CLA/POPC/CAL (48:28:24) bilayer at 313 K (ECC-lipids, GROMACS 5.1.4, 133 ns) [NMRlipids simulation 347] + name: Molecular dynamics trajectory of a CLA/POPC/CAL (48:28:24) bilayer at 313 + K (ECC-lipids, GROMACS 5.1.4, 133 ns) [NMRlipids simulation 347] alternateName: 128POPC_6232SOL_110CAL_220CLA_313K_TIP4p-FBmodel - description: Molecular dynamics trajectory of a lipid bilayer of 220 CLA (48 mol%), 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 28 mol%) and 110 CAL (24 mol%) at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 133 ns (42410 atoms). Deposited as NMRlipids Databank simulation 347 and available from https://doi.org/10.5281/zenodo.1118980. + description: Molecular dynamics trajectory of a lipid bilayer of 220 CLA (48 mol%), + 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 28 mol%) and 110 CAL + (24 mol%) at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 133 ns (42410 + atoms). Deposited as NMRlipids Databank simulation 347 and available from https://doi.org/10.5281/zenodo.1118980. sameAs: https://doi.org/10.5281/zenodo.1118980 datePublished: '2017-12-19' license: @@ -147,7 +151,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1118980 identifier: 10.5281/zenodo.1118980 url: https://doi.org/10.5281/zenodo.1118980 - name: Simulations Of Popc Lipid Bilayer In Water Solution At Various Nacl And Cacl2 Concentrations Using Ecc-Popc Force Field And Various Water Models + name: Simulations Of Popc Lipid Bilayer In Water Solution At Various Nacl And + Cacl2 Concentrations Using Ecc-Popc Force Field And Various Water Models publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/d82/264/d8226460aca0364206b6167d9785260d71e1c98c/69a1d139b81c429400906f515200e4940d811721/README.yaml b/Simulations/d82/264/d8226460aca0364206b6167d9785260d71e1c98c/69a1d139b81c429400906f515200e4940d811721/README.yaml index daa97f0da2..4a73d19e82 100644 --- a/Simulations/d82/264/d8226460aca0364206b6167d9785260d71e1c98c/69a1d139b81c429400906f515200e4940d811721/README.yaml +++ b/Simulations/d82/264/d8226460aca0364206b6167d9785260d71e1c98c/69a1d139b81c429400906f515200e4940d811721/README.yaml @@ -46,9 +46,12 @@ EXPERIMENT: - 10.1016/j.bbamem.2011.07.022/11 ID: 204 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 313 K (ECC-lipids, GROMACS 5.1.4, 200 ns) [NMRlipids simulation 204] + name: Molecular dynamics trajectory of a POPC bilayer at 313 K (ECC-lipids, GROMACS + 5.1.4, 200 ns) [NMRlipids simulation 204] alternateName: 128POPC_6400SOL_313K_OPC3model - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 200 ns (36352 atoms). Deposited as NMRlipids Databank simulation 204 and available from https://doi.org/10.5281/zenodo.1118980. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 200 ns (36352 atoms). + Deposited as NMRlipids Databank simulation 204 and available from https://doi.org/10.5281/zenodo.1118980. sameAs: https://doi.org/10.5281/zenodo.1118980 datePublished: '2017-12-19' license: @@ -138,7 +141,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1118980 identifier: 10.5281/zenodo.1118980 url: https://doi.org/10.5281/zenodo.1118980 - name: Simulations Of Popc Lipid Bilayer In Water Solution At Various Nacl And Cacl2 Concentrations Using Ecc-Popc Force Field And Various Water Models + name: Simulations Of Popc Lipid Bilayer In Water Solution At Various Nacl And + Cacl2 Concentrations Using Ecc-Popc Force Field And Various Water Models publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/d83/418/d8341882481f7f4762372c4977c06b4a1ce3634b/1ea3606eb89db05b49b6e869701993ae39c9d381/README.yaml b/Simulations/d83/418/d8341882481f7f4762372c4977c06b4a1ce3634b/1ea3606eb89db05b49b6e869701993ae39c9d381/README.yaml index b3934b4a94..86ecd67fb3 100644 --- a/Simulations/d83/418/d8341882481f7f4762372c4977c06b4a1ce3634b/1ea3606eb89db05b49b6e869701993ae39c9d381/README.yaml +++ b/Simulations/d83/418/d8341882481f7f4762372c4977c06b4a1ce3634b/1ea3606eb89db05b49b6e869701993ae39c9d381/README.yaml @@ -60,9 +60,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 585 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPG/SOD/CLA/CAL (24:24:24:18:9) bilayer at 298 K (Lipid17, GROMACS, 198 ns) [NMRlipids simulation 585] + name: Molecular dynamics trajectory of a POPC/POPG/SOD/CLA/CAL (24:24:24:18:9) bilayer + at 298 K (Lipid17, GROMACS, 198 ns) [NMRlipids simulation 585] alternateName: 150POPC_150POPG_31401SOL_57CAL_114CLA_150SOD_298K - description: Molecular dynamics trajectory of a lipid bilayer of 150 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 24 mol%), 150 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 24 mol%), 150 SOD (24 mol%), 114 CLA (18 mol%) and 57 CAL (9 mol%) at 298 K. Simulated with Lipid17 in GROMACS for 198 ns (133674 atoms). Deposited as NMRlipids Databank simulation 585 and available from https://doi.org/10.5281/zenodo.3871590. + description: Molecular dynamics trajectory of a lipid bilayer of 150 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 24 mol%), 150 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 24 mol%), + 150 SOD (24 mol%), 114 CLA (18 mol%) and 57 CAL (9 mol%) at 298 K. Simulated with + Lipid17 in GROMACS for 198 ns (133674 atoms). Deposited as NMRlipids Databank + simulation 585 and available from https://doi.org/10.5281/zenodo.3871590. sameAs: https://doi.org/10.5281/zenodo.3871590 datePublished: '2019-10-28' license: @@ -154,7 +159,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3871590 identifier: 10.5281/zenodo.3871590 url: https://doi.org/10.5281/zenodo.3871590 - name: LIPID17 POPC-POPG 50:50 MD simulation, Na+ counterions and 100mM CaCl2, 298K + name: LIPID17 POPC-POPG 50:50 MD simulation, Na+ counterions and 100mM CaCl2, + 298K publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/d85/02d/d8502dfe8aebfe324777177712eddea6139d9113/efc96649f0d91c635be7690f255867fa024baa4d/README.yaml b/Simulations/d85/02d/d8502dfe8aebfe324777177712eddea6139d9113/efc96649f0d91c635be7690f255867fa024baa4d/README.yaml index 1581f56fb0..d61f328395 100644 --- a/Simulations/d85/02d/d8502dfe8aebfe324777177712eddea6139d9113/efc96649f0d91c635be7690f255867fa024baa4d/README.yaml +++ b/Simulations/d85/02d/d8502dfe8aebfe324777177712eddea6139d9113/efc96649f0d91c635be7690f255867fa024baa4d/README.yaml @@ -51,9 +51,13 @@ EXPERIMENT: CHOL: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a DOPC/CHOL (53:47) bilayer at 333.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 654] + name: Molecular dynamics trajectory of a DOPC/CHOL (53:47) bilayer at 333.15 K (CHARMM36, + GROMACS, 1001 ns) [NMRlipids simulation 654] alternateName: 64DOPC_56CHOL_6000SOL_333K - description: Molecular dynamics trajectory of a lipid bilayer of 64 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, 53 mol%) and 56 CHOL (cholesterol, 47 mol%) at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (30976 atoms). Deposited as NMRlipids Databank simulation 654 and available from https://doi.org/10.5281/zenodo.6943929. + description: Molecular dynamics trajectory of a lipid bilayer of 64 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, + 53 mol%) and 56 CHOL (cholesterol, 47 mol%) at 333.15 K. Simulated with CHARMM36 + in GROMACS for 1001 ns (30976 atoms). Deposited as NMRlipids Databank simulation + 654 and available from https://doi.org/10.5281/zenodo.6943929. sameAs: https://doi.org/10.5281/zenodo.6943929 datePublished: '2022-07-30' license: diff --git a/Simulations/d87/a78/d87a78ec32678473762aebb21acac182b28dd9dc/f03ec6ba87add363b18d0fff9c03213bcafa3753/README.yaml b/Simulations/d87/a78/d87a78ec32678473762aebb21acac182b28dd9dc/f03ec6ba87add363b18d0fff9c03213bcafa3753/README.yaml index 4fbd7a512e..d451dced00 100644 --- a/Simulations/d87/a78/d87a78ec32678473762aebb21acac182b28dd9dc/f03ec6ba87add363b18d0fff9c03213bcafa3753/README.yaml +++ b/Simulations/d87/a78/d87a78ec32678473762aebb21acac182b28dd9dc/f03ec6ba87add363b18d0fff9c03213bcafa3753/README.yaml @@ -41,9 +41,12 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 70 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 303 K (CHARMM36, GROMACS 5.0.6, 500 ns) [NMRlipids simulation 70] + name: Molecular dynamics trajectory of a POPC bilayer at 303 K (CHARMM36, GROMACS + 5.0.6, 500 ns) [NMRlipids simulation 70] alternateName: 128POPC_5120SOL_10A-switch_v1 - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 303 K. Simulated with CHARMM36 in GROMACS 5.0.6 for 500 ns (32512 atoms). Deposited as NMRlipids Databank simulation 70 and available from https://doi.org/10.5281/zenodo.164206. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 303 K. Simulated with CHARMM36 in GROMACS 5.0.6 for 500 ns (32512 atoms). Deposited + as NMRlipids Databank simulation 70 and available from https://doi.org/10.5281/zenodo.164206. sameAs: https://doi.org/10.5281/zenodo.164206 datePublished: '2016-11-01' license: diff --git a/Simulations/d8c/596/d8c5962a1961606bf11d5d8d159df45b5da9a31d/4514cc6549784a6dc5129c8082c492175e7a35b7/README.yaml b/Simulations/d8c/596/d8c5962a1961606bf11d5d8d159df45b5da9a31d/4514cc6549784a6dc5129c8082c492175e7a35b7/README.yaml index 1df412cd6e..81076d558f 100644 --- a/Simulations/d8c/596/d8c5962a1961606bf11d5d8d159df45b5da9a31d/4514cc6549784a6dc5129c8082c492175e7a35b7/README.yaml +++ b/Simulations/d8c/596/d8c5962a1961606bf11d5d8d159df45b5da9a31d/4514cc6549784a6dc5129c8082c492175e7a35b7/README.yaml @@ -45,9 +45,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 803 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 300 K (OPLS4, GROMACS Desmond 2022-2, 480 ns) [NMRlipids simulation 803] + name: Molecular dynamics trajectory of a POPC bilayer at 300 K (OPLS4, GROMACS Desmond + 2022-2, 480 ns) [NMRlipids simulation 803] alternateName: 200POPC_4000SOL_300K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 300 K. Simulated with OPLS4 in GROMACS Desmond 2022-2 for 480 ns (38800 atoms). Deposited as NMRlipids Databank simulation 803 and available from https://doi.org/10.5281/zenodo.10929839. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 300 K. Simulated with OPLS4 in GROMACS Desmond 2022-2 for 480 ns (38800 atoms). + Deposited as NMRlipids Databank simulation 803 and available from https://doi.org/10.5281/zenodo.10929839. sameAs: https://doi.org/10.5281/zenodo.10929839 datePublished: '2024-04-05' license: diff --git a/Simulations/d8d/348/d8d348469625cce7a89646ba7160b7a89655bca9/9ef0a1a56cee2c014dea0be3ed2312ea264ca1e7/README.yaml b/Simulations/d8d/348/d8d348469625cce7a89646ba7160b7a89655bca9/9ef0a1a56cee2c014dea0be3ed2312ea264ca1e7/README.yaml index ac464a54cb..5b9b254045 100644 --- a/Simulations/d8d/348/d8d348469625cce7a89646ba7160b7a89655bca9/9ef0a1a56cee2c014dea0be3ed2312ea264ca1e7/README.yaml +++ b/Simulations/d8d/348/d8d348469625cce7a89646ba7160b7a89655bca9/9ef0a1a56cee2c014dea0be3ed2312ea264ca1e7/README.yaml @@ -41,9 +41,12 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 175 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC bilayer at 318 K (CHARMM36, GROMACS 2016.4, 50 ns) [NMRlipids simulation 175] + name: Molecular dynamics trajectory of a DPPC bilayer at 318 K (CHARMM36, GROMACS + 2016.4, 50 ns) [NMRlipids simulation 175] alternateName: 212DPPC_29826SOL_318K - description: Molecular dynamics trajectory of a lipid bilayer of 212 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) at 318 K. Simulated with CHARMM36 in GROMACS 2016.4 for 50 ns (117038 atoms). Deposited as NMRlipids Databank simulation 175 and available from https://doi.org/10.5281/zenodo.3950029. + description: Molecular dynamics trajectory of a lipid bilayer of 212 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) + at 318 K. Simulated with CHARMM36 in GROMACS 2016.4 for 50 ns (117038 atoms). + Deposited as NMRlipids Databank simulation 175 and available from https://doi.org/10.5281/zenodo.3950029. sameAs: https://doi.org/10.5281/zenodo.3950029 datePublished: '2020-07-20' license: @@ -143,7 +146,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3950029 identifier: 10.5281/zenodo.3950029 url: https://doi.org/10.5281/zenodo.3950029 - name: 212 DPPC Molecules bilayer in pure Water, simulated at temperatures ranging from 288K to 358K + name: 212 DPPC Molecules bilayer in pure Water, simulated at temperatures ranging + from 288K to 358K publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/d92/304/d92304d0469e29cc47a2dc9f8181b3e02e25a5d5/99f26569c2305964284f902a5fe66f58617ad741/README.yaml b/Simulations/d92/304/d92304d0469e29cc47a2dc9f8181b3e02e25a5d5/99f26569c2305964284f902a5fe66f58617ad741/README.yaml index b927cf42c1..4f07494d4e 100644 --- a/Simulations/d92/304/d92304d0469e29cc47a2dc9f8181b3e02e25a5d5/99f26569c2305964284f902a5fe66f58617ad741/README.yaml +++ b/Simulations/d92/304/d92304d0469e29cc47a2dc9f8181b3e02e25a5d5/99f26569c2305964284f902a5fe66f58617ad741/README.yaml @@ -63,9 +63,15 @@ EXPERIMENT: POPE: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a POT/SAPC/POPE/TLCL_0H/CLA (33:25:20:11:10) bilayer at 310 K (CHARMM36, GROMACS, 1000 ns) [NMRlipids simulation 839] + name: Molecular dynamics trajectory of a POT/SAPC/POPE/TLCL_0H/CLA (33:25:20:11:10) + bilayer at 310 K (CHARMM36, GROMACS, 1000 ns) [NMRlipids simulation 839] alternateName: IMMmodel_CHARMM_310K - description: Molecular dynamics trajectory of a lipid bilayer of 117 POT (33 mol%), 90 SAPC (1-stearoyl-2-arachidonoyl-sn-glycero-3-phosphocholine, 25 mol%), 70 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 20 mol%), 40 TLCL_0H (tetralinoleoyl cardiolipin(2−), 11 mol%) and 37 CLA (10 mol%) at 310 K. Simulated with CHARMM36 in GROMACS for 1000 ns (73551 atoms). Deposited as NMRlipids Databank simulation 839 and available from https://doi.org/10.5281/zenodo.16001915. + description: Molecular dynamics trajectory of a lipid bilayer of 117 POT (33 mol%), + 90 SAPC (1-stearoyl-2-arachidonoyl-sn-glycero-3-phosphocholine, 25 mol%), 70 POPE + (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 20 mol%), 40 TLCL_0H (tetralinoleoyl + cardiolipin(2−), 11 mol%) and 37 CLA (10 mol%) at 310 K. Simulated with CHARMM36 + in GROMACS for 1000 ns (73551 atoms). Deposited as NMRlipids Databank simulation + 839 and available from https://doi.org/10.5281/zenodo.16001915. sameAs: https://doi.org/10.5281/zenodo.16001915 datePublished: '2025-07-17' license: diff --git a/Simulations/d93/702/d9370247c9468b63f2c1d64c795b08051f775195/8f80b92eb5371214ccb487d53ce1fb313800076c/README.yaml b/Simulations/d93/702/d9370247c9468b63f2c1d64c795b08051f775195/8f80b92eb5371214ccb487d53ce1fb313800076c/README.yaml index 05cd0ab47c..737ca5a3e9 100644 --- a/Simulations/d93/702/d9370247c9468b63f2c1d64c795b08051f775195/8f80b92eb5371214ccb487d53ce1fb313800076c/README.yaml +++ b/Simulations/d93/702/d9370247c9468b63f2c1d64c795b08051f775195/8f80b92eb5371214ccb487d53ce1fb313800076c/README.yaml @@ -57,9 +57,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 239 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL/CLA/SOD (68:17:7:7) bilayer at 310 K (Slipids with ECC-scaled ions (Kohagen), GROMACS 4.6, 200 ns) [NMRlipids simulation 239] + name: Molecular dynamics trajectory of a POPC/CHOL/CLA/SOD (68:17:7:7) bilayer at + 310 K (Slipids with ECC-scaled ions (Kohagen), GROMACS 4.6, 200 ns) [NMRlipids + simulation 239] alternateName: 50CHOL_200POPC_9000SOL_21SOD_21CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 68 mol%), 50 CHOL (cholesterol, 17 mol%), 21 CLA (7 mol%) and 21 SOD (7 mol%) at 310 K. Simulated with Slipids with ECC-scaled ions (Kohagen) in GROMACS 4.6 for 200 ns (57542 atoms). Deposited as NMRlipids Databank simulation 239 and available from https://doi.org/10.5281/zenodo.259343. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 68 mol%), 50 CHOL (cholesterol, 17 mol%), 21 CLA (7 mol%) and 21 SOD (7 mol%) + at 310 K. Simulated with Slipids with ECC-scaled ions (Kohagen) in GROMACS 4.6 + for 200 ns (57542 atoms). Deposited as NMRlipids Databank simulation 239 and available + from https://doi.org/10.5281/zenodo.259343. sameAs: https://doi.org/10.5281/zenodo.259343 datePublished: '2017-01-24' license: @@ -149,7 +155,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.259343 identifier: 10.5281/zenodo.259343 url: https://doi.org/10.5281/zenodo.259343 - name: Popc With Varying Amounts Of Cholesterol, 130 Mm Of Nacl. Slipids With Ecc-Scaled Ions + name: Popc With Varying Amounts Of Cholesterol, 130 Mm Of Nacl. Slipids With Ecc-Scaled + Ions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/d95/8aa/d958aa18c7ff9c6ee185c8a6495914369c9ddff3/f19ce0584fb464fe3e4f3108133b07c6f7529a50/README.yaml b/Simulations/d95/8aa/d958aa18c7ff9c6ee185c8a6495914369c9ddff3/f19ce0584fb464fe3e4f3108133b07c6f7529a50/README.yaml index 4c598bef42..8116fce60b 100644 --- a/Simulations/d95/8aa/d958aa18c7ff9c6ee185c8a6495914369c9ddff3/f19ce0584fb464fe3e4f3108133b07c6f7529a50/README.yaml +++ b/Simulations/d95/8aa/d958aa18c7ff9c6ee185c8a6495914369c9ddff3/f19ce0584fb464fe3e4f3108133b07c6f7529a50/README.yaml @@ -55,9 +55,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 431 bioschema_properties: - name: Molecular dynamics trajectory of a CLA/POPC/CAL (48:28:24) bilayer at 313 K (ECC-lipids, GROMACS 5.1.4, 300 ns) [NMRlipids simulation 431] + name: Molecular dynamics trajectory of a CLA/POPC/CAL (48:28:24) bilayer at 313 + K (ECC-lipids, GROMACS 5.1.4, 300 ns) [NMRlipids simulation 431] alternateName: 128POPC_6232SOL_110CAL_220CLA_313K - description: Molecular dynamics trajectory of a lipid bilayer of 220 CLA (48 mol%), 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 28 mol%) and 110 CAL (24 mol%) at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 300 ns (36178 atoms). Deposited as NMRlipids Databank simulation 431 and available from https://doi.org/10.5281/zenodo.3335503. + description: Molecular dynamics trajectory of a lipid bilayer of 220 CLA (48 mol%), + 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 28 mol%) and 110 CAL + (24 mol%) at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 300 ns (36178 + atoms). Deposited as NMRlipids Databank simulation 431 and available from https://doi.org/10.5281/zenodo.3335503. sameAs: https://doi.org/10.5281/zenodo.3335503 datePublished: '2017-12-19' license: @@ -149,7 +153,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3335503 identifier: 10.5281/zenodo.3335503 url: https://doi.org/10.5281/zenodo.3335503 - name: Simulations of POPC lipid bilayer in water solution at various NaCl, KCl and CaCl2 concentrations using ECC-POPC force field + name: Simulations of POPC lipid bilayer in water solution at various NaCl, KCl + and CaCl2 concentrations using ECC-POPC force field publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/da3/d85/da3d859f724f78b3b654d485024e5f3cb803dbb6/f99aed4d2d27d16c580928f1e438e7974bade4e6/README.yaml b/Simulations/da3/d85/da3d859f724f78b3b654d485024e5f3cb803dbb6/f99aed4d2d27d16c580928f1e438e7974bade4e6/README.yaml index aab0c5e13c..4854563aef 100644 --- a/Simulations/da3/d85/da3d859f724f78b3b654d485024e5f3cb803dbb6/f99aed4d2d27d16c580928f1e438e7974bade4e6/README.yaml +++ b/Simulations/da3/d85/da3d859f724f78b3b654d485024e5f3cb803dbb6/f99aed4d2d27d16c580928f1e438e7974bade4e6/README.yaml @@ -64,9 +64,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 156 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/DOPC/CHOL/CLA/SOD (40:32:10:9:9) bilayer at 310 K (Slipids for lipids and Smith & Dang for ions, GROMACS 4.6, 200 ns) [NMRlipids simulation 156] + name: Molecular dynamics trajectory of a DPPC/DOPC/CHOL/CLA/SOD (40:32:10:9:9) bilayer + at 310 K (Slipids for lipids and Smith & Dang for ions, GROMACS 4.6, 200 ns) [NMRlipids + simulation 156] alternateName: 204DPPC_52CHOL_166DOPC_16880SOL_46SOD_46CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 204 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 40 mol%), 166 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, 32 mol%), 52 CHOL (cholesterol, 10 mol%), 46 CLA (9 mol%) and 46 SOD (9 mol%) at 310 K. Simulated with Slipids for lipids and Smith & Dang for ions in GROMACS 4.6 for 200 ns (104008 atoms). Deposited as NMRlipids Databank simulation 156 and available from https://doi.org/10.5281/zenodo.259443. + description: Molecular dynamics trajectory of a lipid bilayer of 204 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 40 mol%), 166 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, 32 mol%), 52 CHOL + (cholesterol, 10 mol%), 46 CLA (9 mol%) and 46 SOD (9 mol%) at 310 K. Simulated + with Slipids for lipids and Smith & Dang for ions in GROMACS 4.6 for 200 ns (104008 + atoms). Deposited as NMRlipids Databank simulation 156 and available from https://doi.org/10.5281/zenodo.259443. sameAs: https://doi.org/10.5281/zenodo.259443 datePublished: '2017-01-24' license: diff --git a/Simulations/da6/3c5/da63c5664850de423fc2f2d9c70e8b447bb60644/63ef1f69db1f060e4ae3533bb1d15e589a8eff63/README.yaml b/Simulations/da6/3c5/da63c5664850de423fc2f2d9c70e8b447bb60644/63ef1f69db1f060e4ae3533bb1d15e589a8eff63/README.yaml index ba007a02b8..b5ca8e9219 100644 --- a/Simulations/da6/3c5/da63c5664850de423fc2f2d9c70e8b447bb60644/63ef1f69db1f060e4ae3533bb1d15e589a8eff63/README.yaml +++ b/Simulations/da6/3c5/da63c5664850de423fc2f2d9c70e8b447bb60644/63ef1f69db1f060e4ae3533bb1d15e589a8eff63/README.yaml @@ -44,9 +44,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 587 bioschema_properties: - name: Molecular dynamics trajectory of a DLIPC bilayer at 333.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 587] + name: Molecular dynamics trajectory of a DLIPC bilayer at 333.15 K (CHARMM36, GROMACS, + 1001 ns) [NMRlipids simulation 587] alternateName: 1024DLIPC_51200SOL_333K - description: Molecular dynamics trajectory of a lipid bilayer of 1024 DLIPC (1,2-dilinoleoyl-sn-glycero-3-phosphocholine) at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (290816 atoms). Deposited as NMRlipids Databank simulation 587 and available from https://doi.org/10.5281/zenodo.6943413. + description: Molecular dynamics trajectory of a lipid bilayer of 1024 DLIPC (1,2-dilinoleoyl-sn-glycero-3-phosphocholine) + at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (290816 atoms). Deposited + as NMRlipids Databank simulation 587 and available from https://doi.org/10.5281/zenodo.6943413. sameAs: https://doi.org/10.5281/zenodo.6943413 datePublished: '2022-07-30' license: @@ -134,7 +137,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.6943413 identifier: 10.5281/zenodo.6943413 url: https://doi.org/10.5281/zenodo.6943413 - name: Simulations of different single-component bilayers, three different system sizes + name: Simulations of different single-component bilayers, three different system + sizes publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/da7/fe5/da7fe52f886cf0ff412adc8afca5f18f2b16943b/5137616341fdd3b0fc2441858749032aa1c90dc4/README.yaml b/Simulations/da7/fe5/da7fe52f886cf0ff412adc8afca5f18f2b16943b/5137616341fdd3b0fc2441858749032aa1c90dc4/README.yaml index 0102edcfcb..d9d5ba1fb9 100644 --- a/Simulations/da7/fe5/da7fe52f886cf0ff412adc8afca5f18f2b16943b/5137616341fdd3b0fc2441858749032aa1c90dc4/README.yaml +++ b/Simulations/da7/fe5/da7fe52f886cf0ff412adc8afca5f18f2b16943b/5137616341fdd3b0fc2441858749032aa1c90dc4/README.yaml @@ -45,9 +45,12 @@ EXPERIMENT: - 10.1016/j.bbamem.2011.07.022/11 ID: 360 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 313 K (ECC-lipids, GROMACS 5.1.4, 300 ns) [NMRlipids simulation 360] + name: Molecular dynamics trajectory of a POPC bilayer at 313 K (ECC-lipids, GROMACS + 5.1.4, 300 ns) [NMRlipids simulation 360] alternateName: 128POPC_6400SOL_313K_TIP3pmodel - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 300 ns (36352 atoms). Deposited as NMRlipids Databank simulation 360 and available from https://doi.org/10.5281/zenodo.1118980. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 300 ns (36352 atoms). + Deposited as NMRlipids Databank simulation 360 and available from https://doi.org/10.5281/zenodo.1118980. sameAs: https://doi.org/10.5281/zenodo.1118980 datePublished: '2017-12-19' license: @@ -136,7 +139,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1118980 identifier: 10.5281/zenodo.1118980 url: https://doi.org/10.5281/zenodo.1118980 - name: Simulations Of Popc Lipid Bilayer In Water Solution At Various Nacl And Cacl2 Concentrations Using Ecc-Popc Force Field And Various Water Models + name: Simulations Of Popc Lipid Bilayer In Water Solution At Various Nacl And + Cacl2 Concentrations Using Ecc-Popc Force Field And Various Water Models publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/dae/6ba/dae6bab0cffae15f50bb7f464260f27aeba72062/01781911d39fc463302c15129a24334c57676936/README.yaml b/Simulations/dae/6ba/dae6bab0cffae15f50bb7f464260f27aeba72062/01781911d39fc463302c15129a24334c57676936/README.yaml index 36e1a8f444..3adeeff187 100644 --- a/Simulations/dae/6ba/dae6bab0cffae15f50bb7f464260f27aeba72062/01781911d39fc463302c15129a24334c57676936/README.yaml +++ b/Simulations/dae/6ba/dae6bab0cffae15f50bb7f464260f27aeba72062/01781911d39fc463302c15129a24334c57676936/README.yaml @@ -51,9 +51,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/8 ID: 670 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (62:38) bilayer at 298.15 K (Slipids, GROMACS 2021, 1001 ns) [NMRlipids simulation 670] + name: Molecular dynamics trajectory of a POPC/CHOL (62:38) bilayer at 298.15 K (Slipids, + GROMACS 2021, 1001 ns) [NMRlipids simulation 670] alternateName: Slipids_POPC_CHOL38_L - description: Molecular dynamics trajectory of a lipid bilayer of 1024 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 62 mol%) and 640 CHOL (cholesterol, 38 mol%) at 298.15 K. Simulated with Slipids in GROMACS 2021 for 1001 ns (434176 atoms). Deposited as NMRlipids Databank simulation 670 and available from https://doi.org/10.5281/zenodo.7022749. + description: Molecular dynamics trajectory of a lipid bilayer of 1024 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 62 mol%) and 640 CHOL (cholesterol, 38 mol%) at 298.15 K. Simulated with Slipids + in GROMACS 2021 for 1001 ns (434176 atoms). Deposited as NMRlipids Databank simulation + 670 and available from https://doi.org/10.5281/zenodo.7022749. sameAs: https://doi.org/10.5281/zenodo.7022749 datePublished: '2022-08-23' license: diff --git a/Simulations/db2/939/db2939198ddcea670cd6d6e5b5966951166e21df/cd84678e155b178c67f08373ad8533dae296fafd/README.yaml b/Simulations/db2/939/db2939198ddcea670cd6d6e5b5966951166e21df/cd84678e155b178c67f08373ad8533dae296fafd/README.yaml index b257fcbb21..7ea1530e0c 100644 --- a/Simulations/db2/939/db2939198ddcea670cd6d6e5b5966951166e21df/cd84678e155b178c67f08373ad8533dae296fafd/README.yaml +++ b/Simulations/db2/939/db2939198ddcea670cd6d6e5b5966951166e21df/cd84678e155b178c67f08373ad8533dae296fafd/README.yaml @@ -47,9 +47,12 @@ EXPERIMENT: - 10.1016/j.bbamem.2011.07.022/4 ID: 365 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC bilayer at 323 K (Poger GROMOS 53A6_L, GROMACS 4.0.7, 100 ns) [NMRlipids simulation 365] + name: Molecular dynamics trajectory of a DPPC bilayer at 323 K (Poger GROMOS 53A6_L, + GROMACS 4.0.7, 100 ns) [NMRlipids simulation 365] alternateName: 128DPPC_5841SOL_323K - description: Molecular dynamics trajectory of a lipid bilayer of 128 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) at 323 K. Simulated with Poger GROMOS 53A6_L in GROMACS 4.0.7 for 100 ns (23923 atoms). Deposited as NMRlipids Databank simulation 365 and available from https://doi.org/10.5281/zenodo.14594. + description: Molecular dynamics trajectory of a lipid bilayer of 128 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) + at 323 K. Simulated with Poger GROMOS 53A6_L in GROMACS 4.0.7 for 100 ns (23923 + atoms). Deposited as NMRlipids Databank simulation 365 and available from https://doi.org/10.5281/zenodo.14594. sameAs: https://doi.org/10.5281/zenodo.14594 datePublished: '2015-01-27' license: @@ -141,7 +144,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.14594 identifier: 10.5281/zenodo.14594 url: https://doi.org/10.5281/zenodo.14594 - name: Md Simulation Trajectory And Related Files For Dppc Bilayer In Full Hydration (Poger Gromos 53A6_L, Gromacs 4.0.7, Pme, Traj 1) + name: Md Simulation Trajectory And Related Files For Dppc Bilayer In Full Hydration + (Poger Gromos 53A6_L, Gromacs 4.0.7, Pme, Traj 1) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/db7/593/db75937f89f1e19c02c80be8cff3ef5355893405/02dbf3a96ee559f67f320ccc44d87f1e54597f2e/README.yaml b/Simulations/db7/593/db75937f89f1e19c02c80be8cff3ef5355893405/02dbf3a96ee559f67f320ccc44d87f1e54597f2e/README.yaml index 065bc24663..ec5adac31f 100644 --- a/Simulations/db7/593/db75937f89f1e19c02c80be8cff3ef5355893405/02dbf3a96ee559f67f320ccc44d87f1e54597f2e/README.yaml +++ b/Simulations/db7/593/db75937f89f1e19c02c80be8cff3ef5355893405/02dbf3a96ee559f67f320ccc44d87f1e54597f2e/README.yaml @@ -55,9 +55,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 110 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (37:32:32) bilayer at 313 K (ECC-lipids, GROMACS 5.1.4, 300 ns) [NMRlipids simulation 110] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (37:32:32) bilayer at 313 + K (ECC-lipids, GROMACS 5.1.4, 300 ns) [NMRlipids simulation 110] alternateName: 128POPC_6232SOL_110SOD_110CLA_313K_OPC3model - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 37 mol%), 110 CLA (32 mol%) and 110 SOD (32 mol%) at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 300 ns (36068 atoms). Deposited as NMRlipids Databank simulation 110 and available from https://doi.org/10.5281/zenodo.1118980. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 37 mol%), 110 CLA (32 mol%) and 110 SOD (32 mol%) at 313 K. Simulated with ECC-lipids + in GROMACS 5.1.4 for 300 ns (36068 atoms). Deposited as NMRlipids Databank simulation + 110 and available from https://doi.org/10.5281/zenodo.1118980. sameAs: https://doi.org/10.5281/zenodo.1118980 datePublished: '2017-12-19' license: @@ -147,7 +151,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1118980 identifier: 10.5281/zenodo.1118980 url: https://doi.org/10.5281/zenodo.1118980 - name: Simulations Of Popc Lipid Bilayer In Water Solution At Various Nacl And Cacl2 Concentrations Using Ecc-Popc Force Field And Various Water Models + name: Simulations Of Popc Lipid Bilayer In Water Solution At Various Nacl And + Cacl2 Concentrations Using Ecc-Popc Force Field And Various Water Models publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/dba/7c9/dba7c9b912bca8051ee494231012ffaaf19c8fe0/c74f8453402e2f1010c94f11a5c4c4a45eb9c7d7/README.yaml b/Simulations/dba/7c9/dba7c9b912bca8051ee494231012ffaaf19c8fe0/c74f8453402e2f1010c94f11a5c4c4a45eb9c7d7/README.yaml index f1bd120007..8ceba14abf 100644 --- a/Simulations/dba/7c9/dba7c9b912bca8051ee494231012ffaaf19c8fe0/c74f8453402e2f1010c94f11a5c4c4a45eb9c7d7/README.yaml +++ b/Simulations/dba/7c9/dba7c9b912bca8051ee494231012ffaaf19c8fe0/c74f8453402e2f1010c94f11a5c4c4a45eb9c7d7/README.yaml @@ -55,9 +55,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 343 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/CLA/SOD (82:9:9) bilayer at 323 K (OPLSAA-compatible Berger-DPPC-06, GROMACS 4.6.7, 120 ns) [NMRlipids simulation 343] + name: Molecular dynamics trajectory of a DPPC/CLA/SOD (82:9:9) bilayer at 323 K + (OPLSAA-compatible Berger-DPPC-06, GROMACS 4.6.7, 120 ns) [NMRlipids simulation + 343] alternateName: 72DPPC_2864SOL_8SOD_8CLA_323K - description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 82 mol%), 8 CLA (9 mol%) and 8 SOD (9 mol%) at 323 K. Simulated with OPLSAA-compatible Berger-DPPC-06 in GROMACS 4.6.7 for 120 ns (12208 atoms). Deposited as NMRlipids Databank simulation 343 and available from https://doi.org/10.5281/zenodo.16484. + description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 82 mol%), 8 CLA (9 mol%) and 8 SOD (9 mol%) at 323 K. Simulated with OPLSAA-compatible + Berger-DPPC-06 in GROMACS 4.6.7 for 120 ns (12208 atoms). Deposited as NMRlipids + Databank simulation 343 and available from https://doi.org/10.5281/zenodo.16484. sameAs: https://doi.org/10.5281/zenodo.16484 datePublished: '2015-03-30' license: diff --git a/Simulations/dbd/aaf/dbdaaf4eb7409fe5fd300f5dc06871ab18e6a993/5ef3efb79557f75cef2a985dd3ea5104959cd6d6/README.yaml b/Simulations/dbd/aaf/dbdaaf4eb7409fe5fd300f5dc06871ab18e6a993/5ef3efb79557f75cef2a985dd3ea5104959cd6d6/README.yaml index e1fc29d190..2f1fe9621c 100644 --- a/Simulations/dbd/aaf/dbdaaf4eb7409fe5fd300f5dc06871ab18e6a993/5ef3efb79557f75cef2a985dd3ea5104959cd6d6/README.yaml +++ b/Simulations/dbd/aaf/dbdaaf4eb7409fe5fd300f5dc06871ab18e6a993/5ef3efb79557f75cef2a985dd3ea5104959cd6d6/README.yaml @@ -57,9 +57,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 534 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL/CHOL (43:31:16:11) bilayer at 310 K (Slipids with default Amber ions parameters (type C0), GROMACS 4.6, 2000 ns) [NMRlipids simulation 534] + name: Molecular dynamics trajectory of a POPC/CLA/CAL/CHOL (43:31:16:11) bilayer + at 310 K (Slipids with default Amber ions parameters (type C0), GROMACS 4.6, 2000 + ns) [NMRlipids simulation 534] alternateName: 50CHOL_200POPC_9000SOL_73CAL_146CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 43 mol%), 146 CLA (31 mol%), 73 CAL (16 mol%) and 50 CHOL (cholesterol, 11 mol%) at 310 K. Simulated with Slipids with default Amber ions parameters (type C0) in GROMACS 4.6 for 2000 ns (57719 atoms). Deposited as NMRlipids Databank simulation 534 and available from https://doi.org/10.5281/zenodo.259349. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 43 mol%), 146 CLA (31 mol%), 73 CAL (16 mol%) and 50 CHOL (cholesterol, 11 mol%) + at 310 K. Simulated with Slipids with default Amber ions parameters (type C0) + in GROMACS 4.6 for 2000 ns (57719 atoms). Deposited as NMRlipids Databank simulation + 534 and available from https://doi.org/10.5281/zenodo.259349. sameAs: https://doi.org/10.5281/zenodo.259349 datePublished: '2017-01-24' license: @@ -149,7 +155,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.259349 identifier: 10.5281/zenodo.259349 url: https://doi.org/10.5281/zenodo.259349 - name: Popc With Varying Amounts Of Cholesterol, 450 Mm Of Cacl_2. Slipids With Default Amber Ions + name: Popc With Varying Amounts Of Cholesterol, 450 Mm Of Cacl_2. Slipids With + Default Amber Ions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/dc7/f14/dc7f14a4f247140f07204a8e14f5a2a5ff8f58ca/df63fa3bbb96e0f5fb742ac67341e02a3960e555/README.yaml b/Simulations/dc7/f14/dc7f14a4f247140f07204a8e14f5a2a5ff8f58ca/df63fa3bbb96e0f5fb742ac67341e02a3960e555/README.yaml index f4b3825eee..27527bc1f5 100644 --- a/Simulations/dc7/f14/dc7f14a4f247140f07204a8e14f5a2a5ff8f58ca/df63fa3bbb96e0f5fb742ac67341e02a3960e555/README.yaml +++ b/Simulations/dc7/f14/dc7f14a4f247140f07204a8e14f5a2a5ff8f58ca/df63fa3bbb96e0f5fb742ac67341e02a3960e555/README.yaml @@ -51,9 +51,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 393 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (71:29) bilayer at 298.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 393] + name: Molecular dynamics trajectory of a POPC/CHOL (71:29) bilayer at 298.15 K (CHARMM36, + GROMACS, 1001 ns) [NMRlipids simulation 393] alternateName: 64POPC_26CHOL_4500SOL_298K - description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 71 mol%) and 26 CHOL (cholesterol, 29 mol%) at 298.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (24000 atoms). Deposited as NMRlipids Databank simulation 393 and available from https://doi.org/10.5281/zenodo.5767451. + description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 71 mol%) and 26 CHOL (cholesterol, 29 mol%) at 298.15 K. Simulated with CHARMM36 + in GROMACS for 1001 ns (24000 atoms). Deposited as NMRlipids Databank simulation + 393 and available from https://doi.org/10.5281/zenodo.5767451. sameAs: https://doi.org/10.5281/zenodo.5767451 datePublished: '2021-12-08' license: diff --git a/Simulations/dc9/e79/dc9e79e7bbb30e57f996d7ea9c5b61699c4b5fdf/81be8eabc48be2bc1b9ef528bb3a9ef9528c9213/README.yaml b/Simulations/dc9/e79/dc9e79e7bbb30e57f996d7ea9c5b61699c4b5fdf/81be8eabc48be2bc1b9ef528bb3a9ef9528c9213/README.yaml index b24e61a402..7f78cc3d4b 100644 --- a/Simulations/dc9/e79/dc9e79e7bbb30e57f996d7ea9c5b61699c4b5fdf/81be8eabc48be2bc1b9ef528bb3a9ef9528c9213/README.yaml +++ b/Simulations/dc9/e79/dc9e79e7bbb30e57f996d7ea9c5b61699c4b5fdf/81be8eabc48be2bc1b9ef528bb3a9ef9528c9213/README.yaml @@ -33,9 +33,12 @@ EXPERIMENT: DPPC: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a DPPC bilayer at 333 K (SLIPIDS, GROMACS, 100 ns) [NMRlipids simulation 895] + name: Molecular dynamics trajectory of a DPPC bilayer at 333 K (SLIPIDS, GROMACS, + 100 ns) [NMRlipids simulation 895] alternateName: DPPC - description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) at 333 K. Simulated with SLIPIDS in GROMACS for 100 ns (13347 atoms). Deposited as NMRlipids Databank simulation 895 and available from https://doi.org/10.5281/zenodo.7572990. + description: Molecular dynamics trajectory of a lipid bilayer of 72 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) + at 333 K. Simulated with SLIPIDS in GROMACS for 100 ns (13347 atoms). Deposited + as NMRlipids Databank simulation 895 and available from https://doi.org/10.5281/zenodo.7572990. sameAs: https://doi.org/10.5281/zenodo.7572990 datePublished: '2023-01-26' license: @@ -125,7 +128,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.7572990 identifier: 10.5281/zenodo.7572990 url: https://doi.org/10.5281/zenodo.7572990 - name: 'MD simulation input files and results for ,,Atomistic MD simulations of n-alkanes in a phospholipid bilayer: CHARMM36 versus Slipids"' + name: 'MD simulation input files and results for ,,Atomistic MD simulations of + n-alkanes in a phospholipid bilayer: CHARMM36 versus Slipids"' publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/dd5/308/dd5308a40bfd26f201c552e2b59f3d5f06cce4df/6eb953ad7ec64897df9d9d115f013ad9597cc578/README.yaml b/Simulations/dd5/308/dd5308a40bfd26f201c552e2b59f3d5f06cce4df/6eb953ad7ec64897df9d9d115f013ad9597cc578/README.yaml index cd1b385262..7d96a324f5 100644 --- a/Simulations/dd5/308/dd5308a40bfd26f201c552e2b59f3d5f06cce4df/6eb953ad7ec64897df9d9d115f013ad9597cc578/README.yaml +++ b/Simulations/dd5/308/dd5308a40bfd26f201c552e2b59f3d5f06cce4df/6eb953ad7ec64897df9d9d115f013ad9597cc578/README.yaml @@ -51,9 +51,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 528 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPS/SOD (71:14:14) bilayer at 298 K (CHARMM36, GROMACS, 100 ns) [NMRlipids simulation 528] + name: Molecular dynamics trajectory of a POPC/POPS/SOD (71:14:14) bilayer at 298 + K (CHARMM36, GROMACS, 100 ns) [NMRlipids simulation 528] alternateName: 110POPC_22POPS_22SOD_4620SOL_298K_v1 - description: Molecular dynamics trajectory of a lipid bilayer of 110 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 71 mol%), 22 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 14 mol%) and 22 SOD (14 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for 100 ns (31416 atoms). Deposited as NMRlipids Databank simulation 528 and available from https://doi.org/10.5281/zenodo.1182665. + description: Molecular dynamics trajectory of a lipid bilayer of 110 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 71 mol%), 22 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 14 mol%) + and 22 SOD (14 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for 100 ns (31416 + atoms). Deposited as NMRlipids Databank simulation 528 and available from https://doi.org/10.5281/zenodo.1182665. sameAs: https://doi.org/10.5281/zenodo.1182665 datePublished: '2018-02-21' license: @@ -141,7 +145,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1182665 identifier: 10.5281/zenodo.1182665 url: https://doi.org/10.5281/zenodo.1182665 - name: Charmm36 Pops/Popc Simulations (Versions 1 And 2) 298 K 1.0 Nm Lj Switching With Na Ions + name: Charmm36 Pops/Popc Simulations (Versions 1 And 2) 298 K 1.0 Nm Lj Switching + With Na Ions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/dd8/a34/dd8a34917bfdc634e05da10aa69c5e11f9089400/68d079c2fad50af5c764f0d475d48d180c3660f2/README.yaml b/Simulations/dd8/a34/dd8a34917bfdc634e05da10aa69c5e11f9089400/68d079c2fad50af5c764f0d475d48d180c3660f2/README.yaml index 190aaf8738..c19ad11f20 100644 --- a/Simulations/dd8/a34/dd8a34917bfdc634e05da10aa69c5e11f9089400/68d079c2fad50af5c764f0d475d48d180c3660f2/README.yaml +++ b/Simulations/dd8/a34/dd8a34917bfdc634e05da10aa69c5e11f9089400/68d079c2fad50af5c764f0d475d48d180c3660f2/README.yaml @@ -56,9 +56,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 116 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POT/CLA/POPS (35:32:25:7) bilayer at 298 K (CHARMM36, GROMACS, 150 ns) [NMRlipids simulation 116] + name: Molecular dynamics trajectory of a POPC/POT/CLA/POPS (35:32:25:7) bilayer + at 298 K (CHARMM36, GROMACS, 150 ns) [NMRlipids simulation 116] alternateName: 110POPC_22POPS_4946SOL_101POT_79CLA_298K - description: Molecular dynamics trajectory of a lipid bilayer of 110 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 35 mol%), 101 POT (32 mol%), 79 CLA (25 mol%) and 22 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 7 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for 150 ns (32552 atoms). Deposited as NMRlipids Databank simulation 116 and available from https://doi.org/10.5281/zenodo.1493246. + description: Molecular dynamics trajectory of a lipid bilayer of 110 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 35 mol%), 101 POT (32 mol%), 79 CLA (25 mol%) and 22 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, + 7 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for 150 ns (32552 atoms). + Deposited as NMRlipids Databank simulation 116 and available from https://doi.org/10.5281/zenodo.1493246. sameAs: https://doi.org/10.5281/zenodo.1493246 datePublished: '2018-11-21' license: diff --git a/Simulations/dd9/c59/dd9c5964efd8e2840736332b5a938932f12beebc/ed59622747ff6ef7329188dd62173852cdab20fd/README.yaml b/Simulations/dd9/c59/dd9c5964efd8e2840736332b5a938932f12beebc/ed59622747ff6ef7329188dd62173852cdab20fd/README.yaml index 3b9d27ffd0..778cb9aa8c 100644 --- a/Simulations/dd9/c59/dd9c5964efd8e2840736332b5a938932f12beebc/ed59622747ff6ef7329188dd62173852cdab20fd/README.yaml +++ b/Simulations/dd9/c59/dd9c5964efd8e2840736332b5a938932f12beebc/ed59622747ff6ef7329188dd62173852cdab20fd/README.yaml @@ -50,9 +50,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 247 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/CLA/CAL (48:35:17) bilayer at 293 K (Slipids for lipids and Kohagen for ions, GROMACS 4.6, 800 ns) [NMRlipids simulation 247] + name: Molecular dynamics trajectory of a DPPC/CLA/CAL (48:35:17) bilayer at 293 + K (Slipids for lipids and Kohagen for ions, GROMACS 4.6, 800 ns) [NMRlipids simulation + 247] alternateName: 200DOPC_9000SOL_73CAL_146CLA_293K - description: Molecular dynamics trajectory of a lipid bilayer of 200 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 48 mol%), 146 CLA (35 mol%) and 73 CAL (17 mol%) at 293 K. Simulated with Slipids for lipids and Kohagen for ions in GROMACS 4.6 for 800 ns (53219 atoms). Deposited as NMRlipids Databank simulation 247 and available from https://doi.org/10.5281/zenodo.259443. + description: Molecular dynamics trajectory of a lipid bilayer of 200 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 48 mol%), 146 CLA (35 mol%) and 73 CAL (17 mol%) at 293 K. Simulated with Slipids + for lipids and Kohagen for ions in GROMACS 4.6 for 800 ns (53219 atoms). Deposited + as NMRlipids Databank simulation 247 and available from https://doi.org/10.5281/zenodo.259443. sameAs: https://doi.org/10.5281/zenodo.259443 datePublished: '2017-01-24' license: diff --git a/Simulations/ddb/6f6/ddb6f616802ccd84f18b979b61503f8361c1fb4b/8af44af412b5e63f797a8a9039eed3cea5a5936d/README.yaml b/Simulations/ddb/6f6/ddb6f616802ccd84f18b979b61503f8361c1fb4b/8af44af412b5e63f797a8a9039eed3cea5a5936d/README.yaml index 88a8c2c113..1f6a324298 100644 --- a/Simulations/ddb/6f6/ddb6f616802ccd84f18b979b61503f8361c1fb4b/8af44af412b5e63f797a8a9039eed3cea5a5936d/README.yaml +++ b/Simulations/ddb/6f6/ddb6f616802ccd84f18b979b61503f8361c1fb4b/8af44af412b5e63f797a8a9039eed3cea5a5936d/README.yaml @@ -53,9 +53,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/9 ID: 671 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (53:47) bilayer at 298.15 K (MacRog, GROMACS 2021, 1001 ns) [NMRlipids simulation 671] + name: Molecular dynamics trajectory of a POPC/CHOL (53:47) bilayer at 298.15 K (MacRog, + GROMACS 2021, 1001 ns) [NMRlipids simulation 671] alternateName: MacRog_POPC_CHOL47_L - description: Molecular dynamics trajectory of a lipid bilayer of 1024 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 53 mol%) and 896 CHOL (cholesterol, 47 mol%) at 298.15 K. Simulated with MacRog in GROMACS 2021 for 1001 ns (491520 atoms). Deposited as NMRlipids Databank simulation 671 and available from https://doi.org/10.5281/zenodo.7061800. + description: Molecular dynamics trajectory of a lipid bilayer of 1024 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 53 mol%) and 896 CHOL (cholesterol, 47 mol%) at 298.15 K. Simulated with MacRog + in GROMACS 2021 for 1001 ns (491520 atoms). Deposited as NMRlipids Databank simulation + 671 and available from https://doi.org/10.5281/zenodo.7061800. sameAs: https://doi.org/10.5281/zenodo.7061800 datePublished: '2022-09-08' license: diff --git a/Simulations/ddb/994/ddb9947ea9ad6231f77e936da109f41d523be508/2a56a18a2fc8faaf0c1150c597c2288b7b0c989f/README.yaml b/Simulations/ddb/994/ddb9947ea9ad6231f77e936da109f41d523be508/2a56a18a2fc8faaf0c1150c597c2288b7b0c989f/README.yaml index 34b63590c7..b846d90839 100644 --- a/Simulations/ddb/994/ddb9947ea9ad6231f77e936da109f41d523be508/2a56a18a2fc8faaf0c1150c597c2288b7b0c989f/README.yaml +++ b/Simulations/ddb/994/ddb9947ea9ad6231f77e936da109f41d523be508/2a56a18a2fc8faaf0c1150c597c2288b7b0c989f/README.yaml @@ -50,9 +50,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/3 ID: 672 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (89:11) bilayer at 298.15 K (Slipids, GROMACS 2021, 1001 ns) [NMRlipids simulation 672] + name: Molecular dynamics trajectory of a POPC/CHOL (89:11) bilayer at 298.15 K (Slipids, + GROMACS 2021, 1001 ns) [NMRlipids simulation 672] alternateName: Slipids_POPC_CHOL11_S - description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 89 mol%) and 8 CHOL (cholesterol, 11 mol%) at 298.15 K. Simulated with Slipids in GROMACS 2021 for 1001 ns (19968 atoms). Deposited as NMRlipids Databank simulation 672 and available from https://doi.org/10.5281/zenodo.7022749. + description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 89 mol%) and 8 CHOL (cholesterol, 11 mol%) at 298.15 K. Simulated with Slipids + in GROMACS 2021 for 1001 ns (19968 atoms). Deposited as NMRlipids Databank simulation + 672 and available from https://doi.org/10.5281/zenodo.7022749. sameAs: https://doi.org/10.5281/zenodo.7022749 datePublished: '2022-08-23' license: diff --git a/Simulations/ddb/cf1/ddbcf15f3eb1a20b40db561c09e0947e8fbb0569/e20b9624c784350d8ed0942f4e9422f754583ab7/README.yaml b/Simulations/ddb/cf1/ddbcf15f3eb1a20b40db561c09e0947e8fbb0569/e20b9624c784350d8ed0942f4e9422f754583ab7/README.yaml index e82076342f..92b2980f4b 100644 --- a/Simulations/ddb/cf1/ddbcf15f3eb1a20b40db561c09e0947e8fbb0569/e20b9624c784350d8ed0942f4e9422f754583ab7/README.yaml +++ b/Simulations/ddb/cf1/ddbcf15f3eb1a20b40db561c09e0947e8fbb0569/e20b9624c784350d8ed0942f4e9422f754583ab7/README.yaml @@ -45,9 +45,12 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/1 ID: 164 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 300 K (CHARMM36, GROMACS 2019.5, 460 ns) [NMRlipids simulation 164] + name: Molecular dynamics trajectory of a POPC bilayer at 300 K (CHARMM36, GROMACS + 2019.5, 460 ns) [NMRlipids simulation 164] alternateName: 200POPC_8880SOL_300K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 300 K. Simulated with CHARMM36 in GROMACS 2019.5 for 460 ns (53440 atoms). Deposited as NMRlipids Databank simulation 164 and available from https://doi.org/10.5281/zenodo.6336691. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 300 K. Simulated with CHARMM36 in GROMACS 2019.5 for 460 ns (53440 atoms). + Deposited as NMRlipids Databank simulation 164 and available from https://doi.org/10.5281/zenodo.6336691. sameAs: https://doi.org/10.5281/zenodo.6336691 datePublished: '2022-03-08' license: @@ -137,7 +140,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.6336691 identifier: 10.5281/zenodo.6336691 url: https://doi.org/10.5281/zenodo.6336691 - name: MD simulation of POPC bilayer with CHARMM36 force field. Full hydration 44 w/l. + name: MD simulation of POPC bilayer with CHARMM36 force field. Full hydration + 44 w/l. publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/de2/a6c/de2a6c0a44b6ea3f66d48cd2c3a2078bef40e522/ba62d9fd00947450d5f4d4ff18e126f1c5f004d2/README.yaml b/Simulations/de2/a6c/de2a6c0a44b6ea3f66d48cd2c3a2078bef40e522/ba62d9fd00947450d5f4d4ff18e126f1c5f004d2/README.yaml index 6a87b38cc7..1190f82d60 100644 --- a/Simulations/de2/a6c/de2a6c0a44b6ea3f66d48cd2c3a2078bef40e522/ba62d9fd00947450d5f4d4ff18e126f1c5f004d2/README.yaml +++ b/Simulations/de2/a6c/de2a6c0a44b6ea3f66d48cd2c3a2078bef40e522/ba62d9fd00947450d5f4d4ff18e126f1c5f004d2/README.yaml @@ -51,9 +51,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/8 ID: 673 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (62:38) bilayer at 298.15 K (Lipid17, GROMACS 2021, 1001 ns) [NMRlipids simulation 673] + name: Molecular dynamics trajectory of a POPC/CHOL (62:38) bilayer at 298.15 K (Lipid17, + GROMACS 2021, 1001 ns) [NMRlipids simulation 673] alternateName: Lipid17_POPC_CHOL38_L - description: Molecular dynamics trajectory of a lipid bilayer of 1024 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 62 mol%) and 640 CHOL (cholesterol, 38 mol%) at 298.15 K. Simulated with Lipid17 in GROMACS 2021 for 1001 ns (434176 atoms). Deposited as NMRlipids Databank simulation 673 and available from https://doi.org/10.5281/zenodo.6992065. + description: Molecular dynamics trajectory of a lipid bilayer of 1024 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 62 mol%) and 640 CHOL (cholesterol, 38 mol%) at 298.15 K. Simulated with Lipid17 + in GROMACS 2021 for 1001 ns (434176 atoms). Deposited as NMRlipids Databank simulation + 673 and available from https://doi.org/10.5281/zenodo.6992065. sameAs: https://doi.org/10.5281/zenodo.6992065 datePublished: '2022-08-15' license: diff --git a/Simulations/de8/0d8/de80d83c570966d6151ebe37b1e9400ce857af91/ff5c240330218b299881d6ddcc87f4bb9131bfb3/README.yaml b/Simulations/de8/0d8/de80d83c570966d6151ebe37b1e9400ce857af91/ff5c240330218b299881d6ddcc87f4bb9131bfb3/README.yaml index 8f22f1c905..e91fc42ea9 100644 --- a/Simulations/de8/0d8/de80d83c570966d6151ebe37b1e9400ce857af91/ff5c240330218b299881d6ddcc87f4bb9131bfb3/README.yaml +++ b/Simulations/de8/0d8/de80d83c570966d6151ebe37b1e9400ce857af91/ff5c240330218b299881d6ddcc87f4bb9131bfb3/README.yaml @@ -52,9 +52,13 @@ EXPERIMENT: - 10.1039/C4SM00066H/3 ID: 842 bioschema_properties: - name: Molecular dynamics trajectory of a POPS/SOD (50:50) bilayer at 298 K (PROSECCO, GROMACS, 500 ns) [NMRlipids simulation 842] + name: Molecular dynamics trajectory of a POPS/SOD (50:50) bilayer at 298 K (PROSECCO, + GROMACS, 500 ns) [NMRlipids simulation 842] alternateName: POPS_prosECCo - description: Molecular dynamics trajectory of a lipid bilayer of 144 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 50 mol%) and 144 SOD (50 mol%) at 298 K. Simulated with PROSECCO in GROMACS for 500 ns (35712 atoms). Deposited as NMRlipids Databank simulation 842 and available from https://doi.org/10.5281/zenodo.10467181. + description: Molecular dynamics trajectory of a lipid bilayer of 144 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, + 50 mol%) and 144 SOD (50 mol%) at 298 K. Simulated with PROSECCO in GROMACS for + 500 ns (35712 atoms). Deposited as NMRlipids Databank simulation 842 and available + from https://doi.org/10.5281/zenodo.10467181. sameAs: https://doi.org/10.5281/zenodo.10467181 datePublished: '2024-01-07' license: diff --git a/Simulations/deb/035/deb035658c6fe5b1199ffed00ec7cb43d986cb1d/38ef3210d00125cc0ca4daa27f169bf579dc3944/README.yaml b/Simulations/deb/035/deb035658c6fe5b1199ffed00ec7cb43d986cb1d/38ef3210d00125cc0ca4daa27f169bf579dc3944/README.yaml index 59daec92b3..a6598a11a2 100644 --- a/Simulations/deb/035/deb035658c6fe5b1199ffed00ec7cb43d986cb1d/38ef3210d00125cc0ca4daa27f169bf579dc3944/README.yaml +++ b/Simulations/deb/035/deb035658c6fe5b1199ffed00ec7cb43d986cb1d/38ef3210d00125cc0ca4daa27f169bf579dc3944/README.yaml @@ -52,9 +52,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 290 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPE (50:50) bilayer at 300 K (Berger (modified to add a repulsive potential onto the ethanolamine hydrogens), GROMACS, 400 ns) [NMRlipids simulation 290] + name: Molecular dynamics trajectory of a POPC/POPE (50:50) bilayer at 300 K (Berger + (modified to add a repulsive potential onto the ethanolamine hydrogens), GROMACS, + 400 ns) [NMRlipids simulation 290] alternateName: 128POPC_128POPE_11096SOL_300K_Berger - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 50 mol%) and 128 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 50 mol%) at 300 K. Simulated with Berger (modified to add a repulsive potential onto the ethanolamine hydrogens) in GROMACS for 400 ns (46600 atoms). Deposited as NMRlipids Databank simulation 290 and available from https://doi.org/10.5281/zenodo.1402449. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 50 mol%) and 128 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, + 50 mol%) at 300 K. Simulated with Berger (modified to add a repulsive potential + onto the ethanolamine hydrogens) in GROMACS for 400 ns (46600 atoms). Deposited + as NMRlipids Databank simulation 290 and available from https://doi.org/10.5281/zenodo.1402449. sameAs: https://doi.org/10.5281/zenodo.1402449 datePublished: '2018-08-23' license: @@ -103,7 +109,8 @@ bioschema_properties: inDefinedTermSet: http://edamontology.org url: http://edamontology.org/operation_2476 - Molecular dynamics simulation (gromacs) - - Berger (modified to add a repulsive potential onto the ethanolamine hydrogens) force field + - Berger (modified to add a repulsive potential onto the ethanolamine hydrogens) + force field variableMeasured: - '@type': PropertyValue name: area per lipid diff --git a/Simulations/dec/cb5/deccb577ca8ad6e421736887bee86a9205242916/40169c0c0397357618cdad94ea374018fe4bc318/README.yaml b/Simulations/dec/cb5/deccb577ca8ad6e421736887bee86a9205242916/40169c0c0397357618cdad94ea374018fe4bc318/README.yaml index e4018109ae..9842b5c64f 100644 --- a/Simulations/dec/cb5/deccb577ca8ad6e421736887bee86a9205242916/40169c0c0397357618cdad94ea374018fe4bc318/README.yaml +++ b/Simulations/dec/cb5/deccb577ca8ad6e421736887bee86a9205242916/40169c0c0397357618cdad94ea374018fe4bc318/README.yaml @@ -51,9 +51,13 @@ EXPERIMENT: CHOL: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a DOPC/CHOL (89:11) bilayer at 333.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 641] + name: Molecular dynamics trajectory of a DOPC/CHOL (89:11) bilayer at 333.15 K (CHARMM36, + GROMACS, 1001 ns) [NMRlipids simulation 641] alternateName: 64DOPC_8CHOL_3600SOL_333K - description: Molecular dynamics trajectory of a lipid bilayer of 64 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, 89 mol%) and 8 CHOL (cholesterol, 11 mol%) at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (20224 atoms). Deposited as NMRlipids Databank simulation 641 and available from https://doi.org/10.5281/zenodo.6943929. + description: Molecular dynamics trajectory of a lipid bilayer of 64 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, + 89 mol%) and 8 CHOL (cholesterol, 11 mol%) at 333.15 K. Simulated with CHARMM36 + in GROMACS for 1001 ns (20224 atoms). Deposited as NMRlipids Databank simulation + 641 and available from https://doi.org/10.5281/zenodo.6943929. sameAs: https://doi.org/10.5281/zenodo.6943929 datePublished: '2022-07-30' license: diff --git a/Simulations/dfb/5bf/dfb5bf1081781764f77b579e48058942806902e2/3cd2151fd09332fdd650b78a0bc3950479464b08/README.yaml b/Simulations/dfb/5bf/dfb5bf1081781764f77b579e48058942806902e2/3cd2151fd09332fdd650b78a0bc3950479464b08/README.yaml index 261d53be06..d6cfab3a8a 100644 --- a/Simulations/dfb/5bf/dfb5bf1081781764f77b579e48058942806902e2/3cd2151fd09332fdd650b78a0bc3950479464b08/README.yaml +++ b/Simulations/dfb/5bf/dfb5bf1081781764f77b579e48058942806902e2/3cd2151fd09332fdd650b78a0bc3950479464b08/README.yaml @@ -54,9 +54,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 288 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/PAzePCprot (70:30) bilayer at 298 K (Berger, GROMACS 4.5, 50 ns) [NMRlipids simulation 288] + name: Molecular dynamics trajectory of a POPC/PAzePCprot (70:30) bilayer at 298 + K (Berger, GROMACS 4.5, 50 ns) [NMRlipids simulation 288] alternateName: 90POPC_38PAzePCprot_7632SOL_298K - description: Molecular dynamics trajectory of a lipid bilayer of 90 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 70 mol%) and 38 PAzePCprot (1-palmitoyl-2-azelaoyl-sn-glycero-3-phosphocholine protonated, 30 mol%) at 298 K. Simulated with Berger in GROMACS 4.5 for 50 ns (29324 atoms). Deposited as NMRlipids Databank simulation 288 and available from https://doi.org/10.5281/zenodo.44660. + description: Molecular dynamics trajectory of a lipid bilayer of 90 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 70 mol%) and 38 PAzePCprot (1-palmitoyl-2-azelaoyl-sn-glycero-3-phosphocholine + protonated, 30 mol%) at 298 K. Simulated with Berger in GROMACS 4.5 for 50 ns + (29324 atoms). Deposited as NMRlipids Databank simulation 288 and available from + https://doi.org/10.5281/zenodo.44660. sameAs: https://doi.org/10.5281/zenodo.44660 datePublished: '2016-01-12' license: @@ -147,7 +152,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.44660 identifier: 10.5281/zenodo.44660 url: https://doi.org/10.5281/zenodo.44660 - name: MD simulation trajectory and related files for POPC bilayer with 30 mol% of protonated pazePC (Berger, Gromacs 4.5.) + name: MD simulation trajectory and related files for POPC bilayer with 30 mol% + of protonated pazePC (Berger, Gromacs 4.5.) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/e01/6ef/e016ef65b0faacffda0078cec4618647831d2839/e016ef65b0faacffda0078cec4618647831d2839/README.yaml b/Simulations/e01/6ef/e016ef65b0faacffda0078cec4618647831d2839/e016ef65b0faacffda0078cec4618647831d2839/README.yaml index e277a12feb..81c19e8b66 100644 --- a/Simulations/e01/6ef/e016ef65b0faacffda0078cec4618647831d2839/e016ef65b0faacffda0078cec4618647831d2839/README.yaml +++ b/Simulations/e01/6ef/e016ef65b0faacffda0078cec4618647831d2839/e016ef65b0faacffda0078cec4618647831d2839/README.yaml @@ -44,9 +44,13 @@ EXPERIMENT: PAPC: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a PAPC/CLA/POT (92:4:4) bilayer at 303.15 K (CHARMM36m, NAMD 3.0, 500 ns) [NMRlipids simulation 909] + name: Molecular dynamics trajectory of a PAPC/CLA/POT (92:4:4) bilayer at 303.15 + K (CHARMM36m, NAMD 3.0, 500 ns) [NMRlipids simulation 909] alternateName: PAPC 16:0 Deu - description: Molecular dynamics trajectory of a lipid bilayer of 200 PAPC (1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine, 92 mol%), 9 CLA (4 mol%) and 9 POT (4 mol%) at 303.15 K. Simulated with CHARMM36m in NAMD 3.0 for 500 ns (53818 atoms). Deposited as NMRlipids Databank simulation 909 and available from https://doi.org/10.5281/zenodo.18471806. + description: Molecular dynamics trajectory of a lipid bilayer of 200 PAPC (1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine, + 92 mol%), 9 CLA (4 mol%) and 9 POT (4 mol%) at 303.15 K. Simulated with CHARMM36m + in NAMD 3.0 for 500 ns (53818 atoms). Deposited as NMRlipids Databank simulation + 909 and available from https://doi.org/10.5281/zenodo.18471806. sameAs: https://doi.org/10.5281/zenodo.18471806 datePublished: '2026-02-03' license: @@ -137,7 +141,9 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.18471806 identifier: 10.5281/zenodo.18471806 url: https://doi.org/10.5281/zenodo.18471806 - name: 'PAPC lipid bilayer: 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine (16:0)(20:4) | Deutrated, 16:0 | 303K, CHARMM36m-WYF forcefield, NAMD 3.0.2, 2* 500 ns' + name: 'PAPC lipid bilayer: 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine + (16:0)(20:4) | Deutrated, 16:0 | 303K, CHARMM36m-WYF forcefield, NAMD 3.0.2, + 2* 500 ns' publisher: Zenodo _source: api: datacite diff --git a/Simulations/e1d/fec/e1dfecd9f7454f213deada1b2f55d6f14c40dbae/2de54b9db011e3edcc4c694282d3889e18ab8a46/README.yaml b/Simulations/e1d/fec/e1dfecd9f7454f213deada1b2f55d6f14c40dbae/2de54b9db011e3edcc4c694282d3889e18ab8a46/README.yaml index bbb54d8768..5bd0f1f8e9 100644 --- a/Simulations/e1d/fec/e1dfecd9f7454f213deada1b2f55d6f14c40dbae/2de54b9db011e3edcc4c694282d3889e18ab8a46/README.yaml +++ b/Simulations/e1d/fec/e1dfecd9f7454f213deada1b2f55d6f14c40dbae/2de54b9db011e3edcc4c694282d3889e18ab8a46/README.yaml @@ -54,9 +54,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 188 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPS/SOD (71:14:14) bilayer at 298 K (Lipid17 and Dang ions, GROMACS 2018.0, 975 ns) [NMRlipids simulation 188] + name: Molecular dynamics trajectory of a POPC/POPS/SOD (71:14:14) bilayer at 298 + K (Lipid17 and Dang ions, GROMACS 2018.0, 975 ns) [NMRlipids simulation 188] alternateName: 60POPC_12POPS_3600SOL_12SOD_298K - description: Molecular dynamics trajectory of a lipid bilayer of 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 71 mol%), 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 14 mol%) and 12 SOD (14 mol%) at 298 K. Simulated with Lipid17 and Dang ions in GROMACS 2018.0 for 975 ns (20376 atoms). Deposited as NMRlipids Databank simulation 188 and available from https://doi.org/10.5281/zenodo.1487761. + description: Molecular dynamics trajectory of a lipid bilayer of 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 71 mol%), 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 14 mol%) + and 12 SOD (14 mol%) at 298 K. Simulated with Lipid17 and Dang ions in GROMACS + 2018.0 for 975 ns (20376 atoms). Deposited as NMRlipids Databank simulation 188 + and available from https://doi.org/10.5281/zenodo.1487761. sameAs: https://doi.org/10.5281/zenodo.1487761 datePublished: '2018-11-14' license: @@ -146,7 +151,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1487761 identifier: 10.5281/zenodo.1487761 url: https://doi.org/10.5281/zenodo.1487761 - name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS with the lipid17 force field, only counterions, and CaCl2 concentrations + name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS + with the lipid17 force field, only counterions, and CaCl2 concentrations publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/e20/8a2/e208a2f0435f9474b59a922deae73aff8d646c28/662f12d507ed9d155ec61736f57e3b94b0722665/README.yaml b/Simulations/e20/8a2/e208a2f0435f9474b59a922deae73aff8d646c28/662f12d507ed9d155ec61736f57e3b94b0722665/README.yaml index f7496b6be0..af50059fb9 100644 --- a/Simulations/e20/8a2/e208a2f0435f9474b59a922deae73aff8d646c28/662f12d507ed9d155ec61736f57e3b94b0722665/README.yaml +++ b/Simulations/e20/8a2/e208a2f0435f9474b59a922deae73aff8d646c28/662f12d507ed9d155ec61736f57e3b94b0722665/README.yaml @@ -50,9 +50,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 572 bioschema_properties: - name: Molecular dynamics trajectory of a CHOL/POPC (50:50) bilayer at 303.15 K (CHARMM36, GROMACS 5.1.2, 201 ns) [NMRlipids simulation 572] + name: Molecular dynamics trajectory of a CHOL/POPC (50:50) bilayer at 303.15 K (CHARMM36, + GROMACS 5.1.2, 201 ns) [NMRlipids simulation 572] alternateName: 80POPC_7200SOL_80CHOL_303.80K - description: Molecular dynamics trajectory of a lipid bilayer of 80 CHOL (cholesterol, 50 mol%) and 80 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 50 mol%) at 303.15 K. Simulated with CHARMM36 in GROMACS 5.1.2 for 201 ns (38240 atoms). Deposited as NMRlipids Databank simulation 572 and available from https://doi.org/10.5281/zenodo.163343. + description: Molecular dynamics trajectory of a lipid bilayer of 80 CHOL (cholesterol, + 50 mol%) and 80 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 50 mol%) + at 303.15 K. Simulated with CHARMM36 in GROMACS 5.1.2 for 201 ns (38240 atoms). + Deposited as NMRlipids Databank simulation 572 and available from https://doi.org/10.5281/zenodo.163343. sameAs: https://doi.org/10.5281/zenodo.163343 datePublished: '2016-10-26' license: @@ -140,7 +144,9 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.163343 identifier: 10.5281/zenodo.163343 url: https://doi.org/10.5281/zenodo.163343 - name: Popc/Cholesterol (50:50) Lipid Membrane, 303K, Charmm36 Force Field From Charmm-Gui, Simulation Files And 200 Ns Trajectory For Gromacs Md Simulation Engine V5.1.2 + name: Popc/Cholesterol (50:50) Lipid Membrane, 303K, Charmm36 Force Field From + Charmm-Gui, Simulation Files And 200 Ns Trajectory For Gromacs Md Simulation + Engine V5.1.2 publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/e24/62a/e2462abc0128804263156d1f68638eb22de0ada6/fd4e6f8ed63c831f7b8bef6c2e22a887e49f73f9/README.yaml b/Simulations/e24/62a/e2462abc0128804263156d1f68638eb22de0ada6/fd4e6f8ed63c831f7b8bef6c2e22a887e49f73f9/README.yaml index 698a20aed5..48965a1d9c 100644 --- a/Simulations/e24/62a/e2462abc0128804263156d1f68638eb22de0ada6/fd4e6f8ed63c831f7b8bef6c2e22a887e49f73f9/README.yaml +++ b/Simulations/e24/62a/e2462abc0128804263156d1f68638eb22de0ada6/fd4e6f8ed63c831f7b8bef6c2e22a887e49f73f9/README.yaml @@ -47,9 +47,13 @@ DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 286 AUTHORS_CONTACT: Antonio Peon bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPG/SOD (54:23:23) bilayer at 310 K (lipid17, GROMACS, 100 ns) [NMRlipids simulation 286] + name: Molecular dynamics trajectory of a POPC/POPG/SOD (54:23:23) bilayer at 310 + K (lipid17, GROMACS, 100 ns) [NMRlipids simulation 286] alternateName: POPC:POPG(7:3)_T310K - description: Molecular dynamics trajectory of a lipid bilayer of 350 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 54 mol%), 150 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 23 mol%) and 150 SOD (23 mol%) at 310 K. Simulated with lipid17 in GROMACS for 100 ns (141100 atoms). Deposited as NMRlipids Databank simulation 286 and available from https://doi.org/10.5281/zenodo.3241243. + description: Molecular dynamics trajectory of a lipid bilayer of 350 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 54 mol%), 150 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 23 mol%) + and 150 SOD (23 mol%) at 310 K. Simulated with lipid17 in GROMACS for 100 ns (141100 + atoms). Deposited as NMRlipids Databank simulation 286 and available from https://doi.org/10.5281/zenodo.3241243. sameAs: https://doi.org/10.5281/zenodo.3241243 datePublished: '2019-06-06' license: diff --git a/Simulations/e2a/a72/e2aa72be7b07054a9344c68e56a4f45396189c4e/3401edf711d1be25d7e0f8d85ba5b2297b1e6a29/README.yaml b/Simulations/e2a/a72/e2aa72be7b07054a9344c68e56a4f45396189c4e/3401edf711d1be25d7e0f8d85ba5b2297b1e6a29/README.yaml index d0a51a5668..de5373aa42 100644 --- a/Simulations/e2a/a72/e2aa72be7b07054a9344c68e56a4f45396189c4e/3401edf711d1be25d7e0f8d85ba5b2297b1e6a29/README.yaml +++ b/Simulations/e2a/a72/e2aa72be7b07054a9344c68e56a4f45396189c4e/3401edf711d1be25d7e0f8d85ba5b2297b1e6a29/README.yaml @@ -45,9 +45,12 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/1 ID: 674 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 298.15 K (MacRog, GROMACS 2021, 1001 ns) [NMRlipids simulation 674] + name: Molecular dynamics trajectory of a POPC bilayer at 298.15 K (MacRog, GROMACS + 2021, 1001 ns) [NMRlipids simulation 674] alternateName: MacRog_POPC_S - description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 298.15 K. Simulated with MacRog in GROMACS 2021 for 1001 ns (18176 atoms). Deposited as NMRlipids Databank simulation 674 and available from https://doi.org/10.5281/zenodo.7061800. + description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 298.15 K. Simulated with MacRog in GROMACS 2021 for 1001 ns (18176 atoms). + Deposited as NMRlipids Databank simulation 674 and available from https://doi.org/10.5281/zenodo.7061800. sameAs: https://doi.org/10.5281/zenodo.7061800 datePublished: '2022-09-08' license: diff --git a/Simulations/e2b/09a/e2b09acaead3655073b4ed768e4a08d879b0042d/bb294604ef4b17df4b59195e2ac600630d33c644/README.yaml b/Simulations/e2b/09a/e2b09acaead3655073b4ed768e4a08d879b0042d/bb294604ef4b17df4b59195e2ac600630d33c644/README.yaml index e2654c8d28..6a9dc42787 100644 --- a/Simulations/e2b/09a/e2b09acaead3655073b4ed768e4a08d879b0042d/bb294604ef4b17df4b59195e2ac600630d33c644/README.yaml +++ b/Simulations/e2b/09a/e2b09acaead3655073b4ed768e4a08d879b0042d/bb294604ef4b17df4b59195e2ac600630d33c644/README.yaml @@ -41,9 +41,12 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/1 AUTHORS_CONTACT: Hoelfich, Jullianne bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 300 K (Parsley 1.3.1, GROMACS, 500 ns) [NMRlipids simulation 838] + name: Molecular dynamics trajectory of a POPC bilayer at 300 K (Parsley 1.3.1, GROMACS, + 500 ns) [NMRlipids simulation 838] alternateName: POPCandTIP3P - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 300 K. Simulated with Parsley 1.3.1 in GROMACS for 500 ns (32512 atoms). Deposited as NMRlipids Databank simulation 838 and available from https://doi.org/10.5281/zenodo.14880880. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 300 K. Simulated with Parsley 1.3.1 in GROMACS for 500 ns (32512 atoms). Deposited + as NMRlipids Databank simulation 838 and available from https://doi.org/10.5281/zenodo.14880880. sameAs: https://doi.org/10.5281/zenodo.14880880 datePublished: '2025-02-17' license: diff --git a/Simulations/e2d/cc5/e2dcc539d664d8edde594ce7b994eba35c3e202c/e2dcc539d664d8edde594ce7b994eba35c3e202c/README.yaml b/Simulations/e2d/cc5/e2dcc539d664d8edde594ce7b994eba35c3e202c/e2dcc539d664d8edde594ce7b994eba35c3e202c/README.yaml index ac3565f286..9c62dc4e95 100644 --- a/Simulations/e2d/cc5/e2dcc539d664d8edde594ce7b994eba35c3e202c/e2dcc539d664d8edde594ce7b994eba35c3e202c/README.yaml +++ b/Simulations/e2d/cc5/e2dcc539d664d8edde594ce7b994eba35c3e202c/e2dcc539d664d8edde594ce7b994eba35c3e202c/README.yaml @@ -46,9 +46,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 737 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (51:33:16) bilayer at 303 K (Charmm-Drude polarizable; system has been equilibriated using Charmm36, OPENMM, 513 ns) [NMRlipids simulation 737] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (51:33:16) bilayer at 303 + K (Charmm-Drude polarizable; system has been equilibriated using Charmm36, OPENMM, + 513 ns) [NMRlipids simulation 737] alternateName: 128POPC_6400SOL_41CaCl2_303K - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 51 mol%), 82 CLA (33 mol%) and 41 CAL (16 mol%) at 303 K. Simulated with Charmm-Drude polarizable; system has been equilibriated using Charmm36 in OPENMM for 513 ns (57078 atoms). Deposited as NMRlipids Databank simulation 737 and available from https://doi.org/10.5281/zenodo.7600827. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 51 mol%), 82 CLA (33 mol%) and 41 CAL (16 mol%) at 303 K. Simulated with Charmm-Drude + polarizable; system has been equilibriated using Charmm36 in OPENMM for 513 ns + (57078 atoms). Deposited as NMRlipids Databank simulation 737 and available from + https://doi.org/10.5281/zenodo.7600827. sameAs: https://doi.org/10.5281/zenodo.7600827 datePublished: '2020-08-21' license: @@ -140,7 +146,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.7600827 identifier: 10.5281/zenodo.7600827 url: https://doi.org/10.5281/zenodo.7600827 - name: Pure POPC Membrane with 350mM CaCl2 simulations using Drude Polarizable Force Field and OpenMM + name: Pure POPC Membrane with 350mM CaCl2 simulations using Drude Polarizable + Force Field and OpenMM publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/e3b/ab0/e3bab01b0ae100b5f4295515568406052a4370fe/a057f4f6e5bcd279a3a4f7904fe4e8091be59647/README.yaml b/Simulations/e3b/ab0/e3bab01b0ae100b5f4295515568406052a4370fe/a057f4f6e5bcd279a3a4f7904fe4e8091be59647/README.yaml index 8453df2e3c..b0c3ba7c4d 100644 --- a/Simulations/e3b/ab0/e3bab01b0ae100b5f4295515568406052a4370fe/a057f4f6e5bcd279a3a4f7904fe4e8091be59647/README.yaml +++ b/Simulations/e3b/ab0/e3bab01b0ae100b5f4295515568406052a4370fe/a057f4f6e5bcd279a3a4f7904fe4e8091be59647/README.yaml @@ -56,9 +56,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 8 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/CLA/SOD/CHOL (74:9:9:9) bilayer at 295 K (Slipids, GROMACS, 689 ns) [NMRlipids simulation 8] + name: Molecular dynamics trajectory of a DPPC/CLA/SOD/CHOL (74:9:9:9) bilayer at + 295 K (Slipids, GROMACS, 689 ns) [NMRlipids simulation 8] alternateName: 1032DPPC_120CHOL_46440SOL_124SOD_124CLA_295K - description: Molecular dynamics trajectory of a lipid bilayer of 1032 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 74 mol%), 124 CLA (9 mol%), 124 SOD (9 mol%) and 120 CHOL (cholesterol, 9 mol%) at 295 K. Simulated with Slipids in GROMACS for 689 ns (282608 atoms). Deposited as NMRlipids Databank simulation 8 and available from https://doi.org/10.5281/zenodo.3539263. + description: Molecular dynamics trajectory of a lipid bilayer of 1032 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 74 mol%), 124 CLA (9 mol%), 124 SOD (9 mol%) and 120 CHOL (cholesterol, 9 mol%) + at 295 K. Simulated with Slipids in GROMACS for 689 ns (282608 atoms). Deposited + as NMRlipids Databank simulation 8 and available from https://doi.org/10.5281/zenodo.3539263. sameAs: https://doi.org/10.5281/zenodo.3539263 datePublished: '2019-11-12' license: diff --git a/Simulations/e3b/ab0/e3bab01b0ae100b5f4295515568406052a4370fe/f2924af7c927625c480f25db2e5b95511f3d123b/README.yaml b/Simulations/e3b/ab0/e3bab01b0ae100b5f4295515568406052a4370fe/f2924af7c927625c480f25db2e5b95511f3d123b/README.yaml index 91b526324c..4132634a7b 100644 --- a/Simulations/e3b/ab0/e3bab01b0ae100b5f4295515568406052a4370fe/f2924af7c927625c480f25db2e5b95511f3d123b/README.yaml +++ b/Simulations/e3b/ab0/e3bab01b0ae100b5f4295515568406052a4370fe/f2924af7c927625c480f25db2e5b95511f3d123b/README.yaml @@ -57,9 +57,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 7 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/CLA/SOD/CHOL (74:9:9:9) bilayer at 295 K (Slipids, GROMACS 4.6, 680 ns) [NMRlipids simulation 7] + name: Molecular dynamics trajectory of a DPPC/CLA/SOD/CHOL (74:9:9:9) bilayer at + 295 K (Slipids, GROMACS 4.6, 680 ns) [NMRlipids simulation 7] alternateName: 1032DPPC_120CHOL_46440SOL_124SOD_124CLA_295K - description: Molecular dynamics trajectory of a lipid bilayer of 1032 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 74 mol%), 124 CLA (9 mol%), 124 SOD (9 mol%) and 120 CHOL (cholesterol, 9 mol%) at 295 K. Simulated with Slipids in GROMACS 4.6 for 680 ns (282608 atoms). Deposited as NMRlipids Databank simulation 7 and available from https://doi.org/10.5281/zenodo.439066. + description: Molecular dynamics trajectory of a lipid bilayer of 1032 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 74 mol%), 124 CLA (9 mol%), 124 SOD (9 mol%) and 120 CHOL (cholesterol, 9 mol%) + at 295 K. Simulated with Slipids in GROMACS 4.6 for 680 ns (282608 atoms). Deposited + as NMRlipids Databank simulation 7 and available from https://doi.org/10.5281/zenodo.439066. sameAs: https://doi.org/10.5281/zenodo.439066 datePublished: '2017-03-29' license: @@ -153,7 +157,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.439066 identifier: 10.5281/zenodo.439066 url: https://doi.org/10.5281/zenodo.439066 - name: Simulations Of Dppc/Cholesterol Bilayers With The Slipids Force Field, Part 1/2 + name: Simulations Of Dppc/Cholesterol Bilayers With The Slipids Force Field, Part + 1/2 publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/e3d/f7c/e3df7c8f0cb871c0f1169bc8cc20c52f3b407c3f/2659efdbf891e83d0e76359e80ebfe0ec0781eaf/README.yaml b/Simulations/e3d/f7c/e3df7c8f0cb871c0f1169bc8cc20c52f3b407c3f/2659efdbf891e83d0e76359e80ebfe0ec0781eaf/README.yaml index 6732657323..ea087cf4b8 100644 --- a/Simulations/e3d/f7c/e3df7c8f0cb871c0f1169bc8cc20c52f3b407c3f/2659efdbf891e83d0e76359e80ebfe0ec0781eaf/README.yaml +++ b/Simulations/e3d/f7c/e3df7c8f0cb871c0f1169bc8cc20c52f3b407c3f/2659efdbf891e83d0e76359e80ebfe0ec0781eaf/README.yaml @@ -50,9 +50,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 877 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (86:7:7) bilayer at 300 K (CHARMM36, GROMACS 2019.5, 475 ns) [NMRlipids simulation 877] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (86:7:7) bilayer at 300 K + (CHARMM36, GROMACS 2019.5, 475 ns) [NMRlipids simulation 877] alternateName: POPC, 44 w/l, 300 K, 0.1 M NaCl - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 86 mol%), 16 CLA (7 mol%) and 16 SOD (7 mol%) at 300 K. Simulated with CHARMM36 in GROMACS 2019.5 for 475 ns (53472 atoms). Deposited as NMRlipids Databank simulation 877 and available from https://doi.org/10.5281/zenodo.6342104. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 86 mol%), 16 CLA (7 mol%) and 16 SOD (7 mol%) at 300 K. Simulated with CHARMM36 + in GROMACS 2019.5 for 475 ns (53472 atoms). Deposited as NMRlipids Databank simulation + 877 and available from https://doi.org/10.5281/zenodo.6342104. sameAs: https://doi.org/10.5281/zenodo.6342104 datePublished: '2022-03-09' license: diff --git a/Simulations/e52/d65/e52d65f1d76f0fc2d36c75954fb730181ed0b98b/92741e0ec7378de94b1de9c43561dd241eedd289/README.yaml b/Simulations/e52/d65/e52d65f1d76f0fc2d36c75954fb730181ed0b98b/92741e0ec7378de94b1de9c43561dd241eedd289/README.yaml index a0dfa85de9..2da0374412 100644 --- a/Simulations/e52/d65/e52d65f1d76f0fc2d36c75954fb730181ed0b98b/92741e0ec7378de94b1de9c43561dd241eedd289/README.yaml +++ b/Simulations/e52/d65/e52d65f1d76f0fc2d36c75954fb730181ed0b98b/92741e0ec7378de94b1de9c43561dd241eedd289/README.yaml @@ -38,9 +38,12 @@ EXPERIMENT: FORMFACTOR: - 10.1016/j.bbamem.2011.07.022/7 bioschema_properties: - name: Molecular dynamics trajectory of a DLPC bilayer at 303 K (CHARMM36/LJ-PME, GROMACS Gromacs 2022, 100 ns) [NMRlipids simulation 916] + name: Molecular dynamics trajectory of a DLPC bilayer at 303 K (CHARMM36/LJ-PME, + GROMACS Gromacs 2022, 100 ns) [NMRlipids simulation 916] alternateName: Fully hydrated DLPC bilayer in SPC/E water (LJ_cutoff=1.2 nm) - description: Molecular dynamics trajectory of a lipid bilayer of 100 DLPC (1,2-dilauroyl-sn-glycero-3-phosphocholine) at 303 K. Simulated with CHARMM36/LJ-PME in GROMACS Gromacs 2022 for 100 ns (23542 atoms). Deposited as NMRlipids Databank simulation 916 and available from https://doi.org/10.5281/zenodo.20579050. + description: Molecular dynamics trajectory of a lipid bilayer of 100 DLPC (1,2-dilauroyl-sn-glycero-3-phosphocholine) + at 303 K. Simulated with CHARMM36/LJ-PME in GROMACS Gromacs 2022 for 100 ns (23542 + atoms). Deposited as NMRlipids Databank simulation 916 and available from https://doi.org/10.5281/zenodo.20579050. sameAs: https://doi.org/10.5281/zenodo.20579050 datePublished: '2026-06-07' license: @@ -131,7 +134,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.20579050 identifier: 10.5281/zenodo.20579050 url: https://doi.org/10.5281/zenodo.20579050 - name: Fully hydrated DLPC bilayer at different temperatures simulated using CHARMM36 with LJ-PME and LJ-cutoff + name: Fully hydrated DLPC bilayer at different temperatures simulated using CHARMM36 + with LJ-PME and LJ-cutoff publisher: Zenodo _source: api: datacite diff --git a/Simulations/e58/57b/e5857bb065f3cc3c09b34c27a606842a86f58515/84d1bcc682993ea5fe5ce9cdf73544a8346f2123/README.yaml b/Simulations/e58/57b/e5857bb065f3cc3c09b34c27a606842a86f58515/84d1bcc682993ea5fe5ce9cdf73544a8346f2123/README.yaml index 2c36d1ab4c..b3f3340747 100644 --- a/Simulations/e58/57b/e5857bb065f3cc3c09b34c27a606842a86f58515/84d1bcc682993ea5fe5ce9cdf73544a8346f2123/README.yaml +++ b/Simulations/e58/57b/e5857bb065f3cc3c09b34c27a606842a86f58515/84d1bcc682993ea5fe5ce9cdf73544a8346f2123/README.yaml @@ -50,9 +50,13 @@ SOFTWARE: gromacs DIR_WRK: /usr/home/bort/Databank ID: 18 bioschema_properties: - name: Molecular dynamics trajectory of a DAPC/CHOL (90:10) bilayer at 285 K (CHARMM36, GROMACS, 1000 ns) [NMRlipids simulation 18] + name: Molecular dynamics trajectory of a DAPC/CHOL (90:10) bilayer at 285 K (CHARMM36, + GROMACS, 1000 ns) [NMRlipids simulation 18] alternateName: 260DAPC_28CHOL_11520SOL_285K - description: Molecular dynamics trajectory of a lipid bilayer of 260 DAPC (1,2-diarachidonoyl-sn-glycero-3-phosphocholine, 90 mol%) and 28 CHOL (cholesterol, 10 mol%) at 285 K. Simulated with CHARMM36 in GROMACS for 1000 ns (72512 atoms). Deposited as NMRlipids Databank simulation 18 and available from https://doi.org/10.5281/zenodo.2653721. + description: Molecular dynamics trajectory of a lipid bilayer of 260 DAPC (1,2-diarachidonoyl-sn-glycero-3-phosphocholine, + 90 mol%) and 28 CHOL (cholesterol, 10 mol%) at 285 K. Simulated with CHARMM36 + in GROMACS for 1000 ns (72512 atoms). Deposited as NMRlipids Databank simulation + 18 and available from https://doi.org/10.5281/zenodo.2653721. sameAs: https://doi.org/10.5281/zenodo.2653721 datePublished: '2019-04-29' license: @@ -141,7 +145,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.2653721 identifier: 10.5281/zenodo.2653721 url: https://doi.org/10.5281/zenodo.2653721 - name: Atomistic simulations of cholesterol in symmetric lipid bilayers with varying degrees of lipid chain unsaturation + name: Atomistic simulations of cholesterol in symmetric lipid bilayers with varying + degrees of lipid chain unsaturation publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/e5f/15c/e5f15cb26e2be129367eb1d86f2e2c9574f41f7a/675cdcbedd33a49977fbdc04da2e1113a80b3f23/README.yaml b/Simulations/e5f/15c/e5f15cb26e2be129367eb1d86f2e2c9574f41f7a/675cdcbedd33a49977fbdc04da2e1113a80b3f23/README.yaml index 0ed6260684..fc798e3d95 100644 --- a/Simulations/e5f/15c/e5f15cb26e2be129367eb1d86f2e2c9574f41f7a/675cdcbedd33a49977fbdc04da2e1113a80b3f23/README.yaml +++ b/Simulations/e5f/15c/e5f15cb26e2be129367eb1d86f2e2c9574f41f7a/675cdcbedd33a49977fbdc04da2e1113a80b3f23/README.yaml @@ -57,9 +57,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 140 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPS/SOD (66:17:17) bilayer at 310 K (Berger, GROMACS, 80 ns) [NMRlipids simulation 140] + name: Molecular dynamics trajectory of a POPC/POPS/SOD (66:17:17) bilayer at 310 + K (Berger, GROMACS, 80 ns) [NMRlipids simulation 140] alternateName: 102POPC_26POPS_26SOD_4290SOL_310K_Berger - description: Molecular dynamics trajectory of a lipid bilayer of 102 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 66 mol%), 26 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 17 mol%) and 26 SOD (17 mol%) at 310 K. Simulated with Berger in GROMACS for 80 ns (19630 atoms). Deposited as NMRlipids Databank simulation 140 and available from https://doi.org/10.5281/zenodo.1475285. + description: Molecular dynamics trajectory of a lipid bilayer of 102 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 66 mol%), 26 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 17 mol%) + and 26 SOD (17 mol%) at 310 K. Simulated with Berger in GROMACS for 80 ns (19630 + atoms). Deposited as NMRlipids Databank simulation 140 and available from https://doi.org/10.5281/zenodo.1475285. sameAs: https://doi.org/10.5281/zenodo.1475285 datePublished: '2018-10-30' license: diff --git a/Simulations/e61/525/e61525dce3f7538ed14d8371ae22cad3e41c3d89/e61525dce3f7538ed14d8371ae22cad3e41c3d89/README.yaml b/Simulations/e61/525/e61525dce3f7538ed14d8371ae22cad3e41c3d89/e61525dce3f7538ed14d8371ae22cad3e41c3d89/README.yaml index 1aaebbbfb2..898c51ccbc 100644 --- a/Simulations/e61/525/e61525dce3f7538ed14d8371ae22cad3e41c3d89/e61525dce3f7538ed14d8371ae22cad3e41c3d89/README.yaml +++ b/Simulations/e61/525/e61525dce3f7538ed14d8371ae22cad3e41c3d89/e61525dce3f7538ed14d8371ae22cad3e41c3d89/README.yaml @@ -49,9 +49,13 @@ EXPERIMENT: POPC: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (36:32:32) bilayer at 303 K (Charmm-Drude polarizable, OPENMM, 220 ns) [NMRlipids simulation 759] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (36:32:32) bilayer at 303 + K (Charmm-Drude polarizable, OPENMM, 220 ns) [NMRlipids simulation 759] alternateName: POPC_1000_NaCl_CHARMMdrude2023_303K - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 36 mol%), 115 CLA (32 mol%) and 115 SOD (32 mol%) at 303 K. Simulated with Charmm-Drude polarizable in OPENMM for 220 ns (57292 atoms). Deposited as NMRlipids Databank simulation 759 and available from https://doi.org/10.5281/zenodo.8000133. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 36 mol%), 115 CLA (32 mol%) and 115 SOD (32 mol%) at 303 K. Simulated with Charmm-Drude + polarizable in OPENMM for 220 ns (57292 atoms). Deposited as NMRlipids Databank + simulation 759 and available from https://doi.org/10.5281/zenodo.8000133. sameAs: https://doi.org/10.5281/zenodo.8000133 datePublished: '2023-06-02' license: @@ -136,7 +140,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.8000133 identifier: 10.5281/zenodo.8000133 url: https://doi.org/10.5281/zenodo.8000133 - name: Pure POPC membrane simulations with 1000 mM NaCl with the CHARMM-Drude2023 force field (OpenMM) + name: Pure POPC membrane simulations with 1000 mM NaCl with the CHARMM-Drude2023 + force field (OpenMM) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/e63/fd3/e63fd31b3ca6b97db084ef48078e21af2293b5e2/e63fd31b3ca6b97db084ef48078e21af2293b5e2/README.yaml b/Simulations/e63/fd3/e63fd31b3ca6b97db084ef48078e21af2293b5e2/e63fd31b3ca6b97db084ef48078e21af2293b5e2/README.yaml index 0f6063d9fa..ebfa0e9361 100644 --- a/Simulations/e63/fd3/e63fd31b3ca6b97db084ef48078e21af2293b5e2/e63fd31b3ca6b97db084ef48078e21af2293b5e2/README.yaml +++ b/Simulations/e63/fd3/e63fd31b3ca6b97db084ef48078e21af2293b5e2/e63fd31b3ca6b97db084ef48078e21af2293b5e2/README.yaml @@ -47,9 +47,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 137 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (70:30) bilayer at 303 K (CHARMM36 additive force field parameters, OPENMM v7, 100 ns) [NMRlipids simulation 137] + name: Molecular dynamics trajectory of a POPC/CHOL (70:30) bilayer at 303 K (CHARMM36 + additive force field parameters, OPENMM v7, 100 ns) [NMRlipids simulation 137] alternateName: 84POPC_36CHOL_4800SOL_303K - description: Molecular dynamics trajectory of a lipid bilayer of 84 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 70 mol%) and 36 CHOL (cholesterol, 30 mol%) at 303 K. Simulated with CHARMM36 additive force field parameters in OPENMM v7 for 100 ns (28320 atoms). Deposited as NMRlipids Databank simulation 137 and available from https://doi.org/10.5281/zenodo.209360. + description: Molecular dynamics trajectory of a lipid bilayer of 84 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 70 mol%) and 36 CHOL (cholesterol, 30 mol%) at 303 K. Simulated with CHARMM36 + additive force field parameters in OPENMM v7 for 100 ns (28320 atoms). Deposited + as NMRlipids Databank simulation 137 and available from https://doi.org/10.5281/zenodo.209360. sameAs: https://doi.org/10.5281/zenodo.209360 datePublished: '2016-12-19' license: @@ -138,7 +142,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.209360 identifier: 10.5281/zenodo.209360 url: https://doi.org/10.5281/zenodo.209360 - name: Popc/Cholesterol (70:30) Lipid Membrane, 303K, Charmm36 Force Field, Simulation Files And 100 Ns Trajectory For Openmm Simulation Engine V7 + name: Popc/Cholesterol (70:30) Lipid Membrane, 303K, Charmm36 Force Field, Simulation + Files And 100 Ns Trajectory For Openmm Simulation Engine V7 publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/e6b/55b/e6b55b60b48d2c679fda994c839378b8b3c3cab7/314693f7cfbf38021775096965b8cf8cd57439b0/README.yaml b/Simulations/e6b/55b/e6b55b60b48d2c679fda994c839378b8b3c3cab7/314693f7cfbf38021775096965b8cf8cd57439b0/README.yaml index 9377d73c70..437f01327d 100644 --- a/Simulations/e6b/55b/e6b55b60b48d2c679fda994c839378b8b3c3cab7/314693f7cfbf38021775096965b8cf8cd57439b0/README.yaml +++ b/Simulations/e6b/55b/e6b55b60b48d2c679fda994c839378b8b3c3cab7/314693f7cfbf38021775096965b8cf8cd57439b0/README.yaml @@ -63,9 +63,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 218 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/POPS/SOD/CAL (56:15:11:11:7) bilayer at 298 K (ECC-lipids, SPC/E water model, ECC-ions, GROMACS 2018.0, 1000 ns) [NMRlipids simulation 218] + name: Molecular dynamics trajectory of a POPC/CLA/POPS/SOD/CAL (56:15:11:11:7) bilayer + at 298 K (ECC-lipids, SPC/E water model, ECC-ions, GROMACS 2018.0, 1000 ns) [NMRlipids + simulation 218] alternateName: 12POPS_60POPC_3561SOL_8CAL_16CLA_12SOD_298K - description: Molecular dynamics trajectory of a lipid bilayer of 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 56 mol%), 16 CLA (15 mol%), 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 11 mol%), 12 SOD (11 mol%) and 8 CAL (7 mol%) at 298 K. Simulated with ECC-lipids, SPC/E water model, ECC-ions in GROMACS 2018.0 for 1000 ns (20283 atoms). Deposited as NMRlipids Databank simulation 218 and available from https://doi.org/10.5281/zenodo.1488102. + description: Molecular dynamics trajectory of a lipid bilayer of 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 56 mol%), 16 CLA (15 mol%), 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, + 11 mol%), 12 SOD (11 mol%) and 8 CAL (7 mol%) at 298 K. Simulated with ECC-lipids, + SPC/E water model, ECC-ions in GROMACS 2018.0 for 1000 ns (20283 atoms). Deposited + as NMRlipids Databank simulation 218 and available from https://doi.org/10.5281/zenodo.1488102. sameAs: https://doi.org/10.5281/zenodo.1488102 datePublished: '2018-11-14' license: @@ -158,7 +164,9 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1488102 identifier: 10.5281/zenodo.1488102 url: https://doi.org/10.5281/zenodo.1488102 - name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS (5:1) with ECC-lipids force field, and Na+ (K+) counterions at various CaCl2 additional concentrations + name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS + (5:1) with ECC-lipids force field, and Na+ (K+) counterions at various CaCl2 + additional concentrations publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/e6c/834/e6c834e53bc624e7861a7b60dd5c68767af53cc1/ba5f536a0370e05367045f5a329a37244cb6ecc1/README.yaml b/Simulations/e6c/834/e6c834e53bc624e7861a7b60dd5c68767af53cc1/ba5f536a0370e05367045f5a329a37244cb6ecc1/README.yaml index fb1412c9ca..7a67c24067 100644 --- a/Simulations/e6c/834/e6c834e53bc624e7861a7b60dd5c68767af53cc1/ba5f536a0370e05367045f5a329a37244cb6ecc1/README.yaml +++ b/Simulations/e6c/834/e6c834e53bc624e7861a7b60dd5c68767af53cc1/ba5f536a0370e05367045f5a329a37244cb6ecc1/README.yaml @@ -60,9 +60,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 217 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/POPG/SOD/CAL (52:14:13:13:7) bilayer at 298 K (Lipid17, GROMACS, 250 ns) [NMRlipids simulation 217] + name: Molecular dynamics trajectory of a POPC/CLA/POPG/SOD/CAL (52:14:13:13:7) bilayer + at 298 K (Lipid17, GROMACS, 250 ns) [NMRlipids simulation 217] alternateName: 350POPC_88POPG_26124SOL_47CAL_94CLA_88SOD_298K - description: Molecular dynamics trajectory of a lipid bilayer of 350 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 52 mol%), 94 CLA (14 mol%), 88 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 13 mol%), 88 SOD (13 mol%) and 47 CAL (7 mol%) at 298 K. Simulated with Lipid17 in GROMACS for 250 ns (136677 atoms). Deposited as NMRlipids Databank simulation 217 and available from https://doi.org/10.5281/zenodo.3833725. + description: Molecular dynamics trajectory of a lipid bilayer of 350 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 52 mol%), 94 CLA (14 mol%), 88 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, + 13 mol%), 88 SOD (13 mol%) and 47 CAL (7 mol%) at 298 K. Simulated with Lipid17 + in GROMACS for 250 ns (136677 atoms). Deposited as NMRlipids Databank simulation + 217 and available from https://doi.org/10.5281/zenodo.3833725. sameAs: https://doi.org/10.5281/zenodo.3833725 datePublished: '2019-10-23' license: @@ -154,7 +159,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3833725 identifier: 10.5281/zenodo.3833725 url: https://doi.org/10.5281/zenodo.3833725 - name: LIPID17 POPC-POPG 80:20 MD simulation, Na+ counterions and 100mM CaCl2, 298K + name: LIPID17 POPC-POPG 80:20 MD simulation, Na+ counterions and 100mM CaCl2, + 298K publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/e6f/dde/e6fdde993fda386ebdfae3a429f94172f8cefd6f/931bba90c11699a1da26d12352e084d20424172e/README.yaml b/Simulations/e6f/dde/e6fdde993fda386ebdfae3a429f94172f8cefd6f/931bba90c11699a1da26d12352e084d20424172e/README.yaml index 33cb258925..9ec35baf34 100644 --- a/Simulations/e6f/dde/e6fdde993fda386ebdfae3a429f94172f8cefd6f/931bba90c11699a1da26d12352e084d20424172e/README.yaml +++ b/Simulations/e6f/dde/e6fdde993fda386ebdfae3a429f94172f8cefd6f/931bba90c11699a1da26d12352e084d20424172e/README.yaml @@ -50,9 +50,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 342 bioschema_properties: - name: Molecular dynamics trajectory of a DSPC/CLA/SOD (82:9:9) bilayer at 338 K (CHARMM36, GROMACS 5.0.4, 500 ns) [NMRlipids simulation 342] + name: Molecular dynamics trajectory of a DSPC/CLA/SOD (82:9:9) bilayer at 338 K + (CHARMM36, GROMACS 5.0.4, 500 ns) [NMRlipids simulation 342] alternateName: 512DSPC_20480SOL_55SOD_55CLA_338K - description: Molecular dynamics trajectory of a lipid bilayer of 512 DSPC (1,2-distearoyl-sn-glycero-3-phosphocholine, 82 mol%), 55 CLA (9 mol%) and 55 SOD (9 mol%) at 338 K. Simulated with CHARMM36 in GROMACS 5.0.4 for 500 ns (134254 atoms). Deposited as NMRlipids Databank simulation 342 and available from https://doi.org/10.5281/zenodo.1009094. + description: Molecular dynamics trajectory of a lipid bilayer of 512 DSPC (1,2-distearoyl-sn-glycero-3-phosphocholine, + 82 mol%), 55 CLA (9 mol%) and 55 SOD (9 mol%) at 338 K. Simulated with CHARMM36 + in GROMACS 5.0.4 for 500 ns (134254 atoms). Deposited as NMRlipids Databank simulation + 342 and available from https://doi.org/10.5281/zenodo.1009094. sameAs: https://doi.org/10.5281/zenodo.1009094 datePublished: '2017-10-11' license: diff --git a/Simulations/e73/1ae/e731aed54224afda560e6ed02db66a7a9108dc6f/345ac370b6c2c394f018a6421b5c4a09e41579fe/README.yaml b/Simulations/e73/1ae/e731aed54224afda560e6ed02db66a7a9108dc6f/345ac370b6c2c394f018a6421b5c4a09e41579fe/README.yaml index 6263441a0e..d326b7c2b9 100644 --- a/Simulations/e73/1ae/e731aed54224afda560e6ed02db66a7a9108dc6f/345ac370b6c2c394f018a6421b5c4a09e41579fe/README.yaml +++ b/Simulations/e73/1ae/e731aed54224afda560e6ed02db66a7a9108dc6f/345ac370b6c2c394f018a6421b5c4a09e41579fe/README.yaml @@ -50,9 +50,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 153 bioschema_properties: - name: Molecular dynamics trajectory of a POPG/SOD (50:50) bilayer at 310 K (GROMOS-CKP, GROMACS 2018.3, 100 ns) [NMRlipids simulation 153] + name: Molecular dynamics trajectory of a POPG/SOD (50:50) bilayer at 310 K (GROMOS-CKP, + GROMACS 2018.3, 100 ns) [NMRlipids simulation 153] alternateName: 500POPG_25000SOL_500SOD_310K_GROMOS-CKP - description: Molecular dynamics trajectory of a lipid bilayer of 500 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 50 mol%) and 500 SOD (50 mol%) at 310 K. Simulated with GROMOS-CKP in GROMACS 2018.3 for 100 ns (102000 atoms). Deposited as NMRlipids Databank simulation 153 and available from https://doi.org/10.5281/zenodo.3484548. + description: Molecular dynamics trajectory of a lipid bilayer of 500 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, + 50 mol%) and 500 SOD (50 mol%) at 310 K. Simulated with GROMOS-CKP in GROMACS + 2018.3 for 100 ns (102000 atoms). Deposited as NMRlipids Databank simulation 153 + and available from https://doi.org/10.5281/zenodo.3484548. sameAs: https://doi.org/10.5281/zenodo.3484548 datePublished: '2019-06-03' license: diff --git a/Simulations/e7b/a4b/e7ba4b167ed159f63ce55d7a6e6e7536d9fe93cd/48cb3719c54af93939a92567b276f9042a9abaf6/README.yaml b/Simulations/e7b/a4b/e7ba4b167ed159f63ce55d7a6e6e7536d9fe93cd/48cb3719c54af93939a92567b276f9042a9abaf6/README.yaml index 621e043db4..304c08c7c1 100644 --- a/Simulations/e7b/a4b/e7ba4b167ed159f63ce55d7a6e6e7536d9fe93cd/48cb3719c54af93939a92567b276f9042a9abaf6/README.yaml +++ b/Simulations/e7b/a4b/e7ba4b167ed159f63ce55d7a6e6e7536d9fe93cd/48cb3719c54af93939a92567b276f9042a9abaf6/README.yaml @@ -49,9 +49,12 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/1 ID: 202 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 298 K (GROMOS-CKP, GROMACS, 350 ns) [NMRlipids simulation 202] + name: Molecular dynamics trajectory of a POPC bilayer at 298 K (GROMOS-CKP, GROMACS, + 350 ns) [NMRlipids simulation 202] alternateName: POPC_298 - description: Molecular dynamics trajectory of a lipid bilayer of 500 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 298 K. Simulated with GROMOS-CKP in GROMACS for 350 ns (101000 atoms). Deposited as NMRlipids Databank simulation 202 and available from https://doi.org/10.5281/zenodo.5997385. + description: Molecular dynamics trajectory of a lipid bilayer of 500 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 298 K. Simulated with GROMOS-CKP in GROMACS for 350 ns (101000 atoms). Deposited + as NMRlipids Databank simulation 202 and available from https://doi.org/10.5281/zenodo.5997385. sameAs: https://doi.org/10.5281/zenodo.5997385 datePublished: '2022-02-07' license: diff --git a/Simulations/e84/07b/e8407b239675f26c78c8b9d6f98ba2c337a9650b/3b81ee62d6b3966877fa94b6dec9ffcdb7af7ade/README.yaml b/Simulations/e84/07b/e8407b239675f26c78c8b9d6f98ba2c337a9650b/3b81ee62d6b3966877fa94b6dec9ffcdb7af7ade/README.yaml index a02af8d38b..c236920ed2 100644 --- a/Simulations/e84/07b/e8407b239675f26c78c8b9d6f98ba2c337a9650b/3b81ee62d6b3966877fa94b6dec9ffcdb7af7ade/README.yaml +++ b/Simulations/e84/07b/e8407b239675f26c78c8b9d6f98ba2c337a9650b/3b81ee62d6b3966877fa94b6dec9ffcdb7af7ade/README.yaml @@ -49,9 +49,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 469 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (45:27:27) bilayer at 298.15 K (Lipid14 for lipids and AMBER99SB-ILDN for ions, GROMACS 5.0.3, 100 ns) [NMRlipids simulation 469] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (45:27:27) bilayer at 298.15 + K (Lipid14 for lipids and AMBER99SB-ILDN for ions, GROMACS 5.0.3, 100 ns) [NMRlipids + simulation 469] alternateName: 128POPC_5120SOL_77SOD_77CLA_298K - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 45 mol%), 77 CLA (27 mol%) and 77 SOD (27 mol%) at 298.15 K. Simulated with Lipid14 for lipids and AMBER99SB-ILDN for ions in GROMACS 5.0.3 for 100 ns (32666 atoms). Deposited as NMRlipids Databank simulation 469 and available from https://doi.org/10.5281/zenodo.30865. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 45 mol%), 77 CLA (27 mol%) and 77 SOD (27 mol%) at 298.15 K. Simulated with Lipid14 + for lipids and AMBER99SB-ILDN for ions in GROMACS 5.0.3 for 100 ns (32666 atoms). + Deposited as NMRlipids Databank simulation 469 and available from https://doi.org/10.5281/zenodo.30865. sameAs: https://doi.org/10.5281/zenodo.30865 datePublished: '2015-09-11' license: diff --git a/Simulations/e85/9ac/e859acb19b28003d353bf285516b6c978a8043cc/5b37230ffd595558eb9e9b2e5e82a47a223a34c2/README.yaml b/Simulations/e85/9ac/e859acb19b28003d353bf285516b6c978a8043cc/5b37230ffd595558eb9e9b2e5e82a47a223a34c2/README.yaml index cb3ec658d2..2a14235f3d 100644 --- a/Simulations/e85/9ac/e859acb19b28003d353bf285516b6c978a8043cc/5b37230ffd595558eb9e9b2e5e82a47a223a34c2/README.yaml +++ b/Simulations/e85/9ac/e859acb19b28003d353bf285516b6c978a8043cc/5b37230ffd595558eb9e9b2e5e82a47a223a34c2/README.yaml @@ -56,9 +56,14 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 580 bioschema_properties: - name: Molecular dynamics trajectory of a CLA/POPC/CAL/POPS (42:28:24:6) bilayer at 298 K (CHARMM36, GROMACS, 200 ns) [NMRlipids simulation 580] + name: Molecular dynamics trajectory of a CLA/POPC/CAL/POPS (42:28:24:6) bilayer + at 298 K (CHARMM36, GROMACS, 200 ns) [NMRlipids simulation 580] alternateName: 250POPC_50POPS_214CAL_378CLA_298K_73964Atoms - description: Molecular dynamics trajectory of a lipid bilayer of 378 CLA (42 mol%), 250 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 28 mol%), 214 CAL (24 mol%) and 50 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 6 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for 200 ns (73964 atoms). Deposited as NMRlipids Databank simulation 580 and available from https://doi.org/10.5281/zenodo.2542135. + description: Molecular dynamics trajectory of a lipid bilayer of 378 CLA (42 mol%), + 250 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 28 mol%), 214 CAL + (24 mol%) and 50 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 6 mol%) + at 298 K. Simulated with CHARMM36 in GROMACS for 200 ns (73964 atoms). Deposited + as NMRlipids Databank simulation 580 and available from https://doi.org/10.5281/zenodo.2542135. sameAs: https://doi.org/10.5281/zenodo.2542135 datePublished: '2019-01-16' license: diff --git a/Simulations/e8e/789/e8e789ae73225f6e71034f68224d10f599bfbf13/0be719df4c0630bd9df1a8e9d52943ec8f6cd6e7/README.yaml b/Simulations/e8e/789/e8e789ae73225f6e71034f68224d10f599bfbf13/0be719df4c0630bd9df1a8e9d52943ec8f6cd6e7/README.yaml index aa0395542e..3099e0514c 100644 --- a/Simulations/e8e/789/e8e789ae73225f6e71034f68224d10f599bfbf13/0be719df4c0630bd9df1a8e9d52943ec8f6cd6e7/README.yaml +++ b/Simulations/e8e/789/e8e789ae73225f6e71034f68224d10f599bfbf13/0be719df4c0630bd9df1a8e9d52943ec8f6cd6e7/README.yaml @@ -42,9 +42,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 515 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 310 K (Slipids, GROMACS 4.6, 500 ns) [NMRlipids simulation 515] + name: Molecular dynamics trajectory of a POPC bilayer at 310 K (Slipids, GROMACS + 4.6, 500 ns) [NMRlipids simulation 515] alternateName: 200POPC_9000SOL_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 310 K. Simulated with Slipids in GROMACS 4.6 for 500 ns (53800 atoms). Deposited as NMRlipids Databank simulation 515 and available from https://doi.org/10.5281/zenodo.3243328. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 310 K. Simulated with Slipids in GROMACS 4.6 for 500 ns (53800 atoms). Deposited + as NMRlipids Databank simulation 515 and available from https://doi.org/10.5281/zenodo.3243328. sameAs: https://doi.org/10.5281/zenodo.3243328 datePublished: '2016-08-22' license: @@ -131,7 +134,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3243328 identifier: 10.5281/zenodo.3243328 url: https://doi.org/10.5281/zenodo.3243328 - name: POPC with 0, 10, 20, and 30 mol-% of cholesterol at 310 K. Slipids force field. + name: POPC with 0, 10, 20, and 30 mol-% of cholesterol at 310 K. Slipids force + field. publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/e8e/c33/e8ec33068624b5dd21710da1f8ce2d179d107187/6c41c5e384d057686b19566f51345ab165d740dd/README.yaml b/Simulations/e8e/c33/e8ec33068624b5dd21710da1f8ce2d179d107187/6c41c5e384d057686b19566f51345ab165d740dd/README.yaml index d62f3e08bc..2a375351ec 100644 --- a/Simulations/e8e/c33/e8ec33068624b5dd21710da1f8ce2d179d107187/6c41c5e384d057686b19566f51345ab165d740dd/README.yaml +++ b/Simulations/e8e/c33/e8ec33068624b5dd21710da1f8ce2d179d107187/6c41c5e384d057686b19566f51345ab165d740dd/README.yaml @@ -51,9 +51,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 514 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPS/POT (71:14:14) bilayer at 298 K (CHARMM36, GROMACS, 100 ns) [NMRlipids simulation 514] + name: Molecular dynamics trajectory of a POPC/POPS/POT (71:14:14) bilayer at 298 + K (CHARMM36, GROMACS, 100 ns) [NMRlipids simulation 514] alternateName: 110POPC_22POPS_22POT_4620SOL_298K_v2 - description: Molecular dynamics trajectory of a lipid bilayer of 110 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 71 mol%), 22 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 14 mol%) and 22 POT (14 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for 100 ns (31416 atoms). Deposited as NMRlipids Databank simulation 514 and available from https://doi.org/10.5281/zenodo.1182658. + description: Molecular dynamics trajectory of a lipid bilayer of 110 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 71 mol%), 22 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 14 mol%) + and 22 POT (14 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for 100 ns (31416 + atoms). Deposited as NMRlipids Databank simulation 514 and available from https://doi.org/10.5281/zenodo.1182658. sameAs: https://doi.org/10.5281/zenodo.1182658 datePublished: '2018-02-21' license: @@ -141,7 +145,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1182658 identifier: 10.5281/zenodo.1182658 url: https://doi.org/10.5281/zenodo.1182658 - name: Charmm36 Pops/Popc Simulations (Versions 1 And 2) 298 K 1.0 Nm Lj Switching With K Ions + name: Charmm36 Pops/Popc Simulations (Versions 1 And 2) 298 K 1.0 Nm Lj Switching + With K Ions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/e90/115/e901157d86188c140ff79175964c186d94a26127/2e62a7728b0e21f8823c5a7cbde37bcc8494229b/README.yaml b/Simulations/e90/115/e901157d86188c140ff79175964c186d94a26127/2e62a7728b0e21f8823c5a7cbde37bcc8494229b/README.yaml index 05b79dac8c..208dd8987f 100644 --- a/Simulations/e90/115/e901157d86188c140ff79175964c186d94a26127/2e62a7728b0e21f8823c5a7cbde37bcc8494229b/README.yaml +++ b/Simulations/e90/115/e901157d86188c140ff79175964c186d94a26127/2e62a7728b0e21f8823c5a7cbde37bcc8494229b/README.yaml @@ -56,9 +56,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 432 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/CHOL/CLA/SOD (70:13:9:9) bilayer at 315 K (Slipids, GROMACS, 1000 ns) [NMRlipids simulation 432] + name: Molecular dynamics trajectory of a DPPC/CHOL/CLA/SOD (70:13:9:9) bilayer at + 315 K (Slipids, GROMACS, 1000 ns) [NMRlipids simulation 432] alternateName: 976DPPC_176CHOL_46440SOL_124SOD_124CLA_315K - description: Molecular dynamics trajectory of a lipid bilayer of 976 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 70 mol%), 176 CHOL (cholesterol, 13 mol%), 124 CLA (9 mol%) and 124 SOD (9 mol%) at 315 K. Simulated with Slipids in GROMACS for 1000 ns (279472 atoms). Deposited as NMRlipids Databank simulation 432 and available from https://doi.org/10.5281/zenodo.3540513. + description: Molecular dynamics trajectory of a lipid bilayer of 976 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 70 mol%), 176 CHOL (cholesterol, 13 mol%), 124 CLA (9 mol%) and 124 SOD (9 mol%) + at 315 K. Simulated with Slipids in GROMACS for 1000 ns (279472 atoms). Deposited + as NMRlipids Databank simulation 432 and available from https://doi.org/10.5281/zenodo.3540513. sameAs: https://doi.org/10.5281/zenodo.3540513 datePublished: '2019-11-13' license: diff --git a/Simulations/e95/22c/e9522c15b02896745581a44703fd2211e0680422/acee48b47743b28e0dfd31437aca72f364c2edd7/README.yaml b/Simulations/e95/22c/e9522c15b02896745581a44703fd2211e0680422/acee48b47743b28e0dfd31437aca72f364c2edd7/README.yaml index fde4d3d52a..64809cfa71 100644 --- a/Simulations/e95/22c/e9522c15b02896745581a44703fd2211e0680422/acee48b47743b28e0dfd31437aca72f364c2edd7/README.yaml +++ b/Simulations/e95/22c/e9522c15b02896745581a44703fd2211e0680422/acee48b47743b28e0dfd31437aca72f364c2edd7/README.yaml @@ -53,9 +53,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/8 ID: 620 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (62:38) bilayer at 298.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 620] + name: Molecular dynamics trajectory of a POPC/CHOL (62:38) bilayer at 298.15 K (CHARMM36, + GROMACS, 1001 ns) [NMRlipids simulation 620] alternateName: 64POPC_40CHOL_5200SOL_298K - description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 62 mol%) and 40 CHOL (cholesterol, 38 mol%) at 298.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (27136 atoms). Deposited as NMRlipids Databank simulation 620 and available from https://doi.org/10.5281/zenodo.5767451. + description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 62 mol%) and 40 CHOL (cholesterol, 38 mol%) at 298.15 K. Simulated with CHARMM36 + in GROMACS for 1001 ns (27136 atoms). Deposited as NMRlipids Databank simulation + 620 and available from https://doi.org/10.5281/zenodo.5767451. sameAs: https://doi.org/10.5281/zenodo.5767451 datePublished: '2021-12-08' license: diff --git a/Simulations/e97/2fb/e972fb7afc0ab78c7004c0971d5055b2a0cdc51f/e972fb7afc0ab78c7004c0971d5055b2a0cdc51f/README.yaml b/Simulations/e97/2fb/e972fb7afc0ab78c7004c0971d5055b2a0cdc51f/e972fb7afc0ab78c7004c0971d5055b2a0cdc51f/README.yaml index 46127f64d0..d0eee8ff62 100644 --- a/Simulations/e97/2fb/e972fb7afc0ab78c7004c0971d5055b2a0cdc51f/e972fb7afc0ab78c7004c0971d5055b2a0cdc51f/README.yaml +++ b/Simulations/e97/2fb/e972fb7afc0ab78c7004c0971d5055b2a0cdc51f/e972fb7afc0ab78c7004c0971d5055b2a0cdc51f/README.yaml @@ -41,9 +41,12 @@ EXPERIMENT: - 10.1016/j.bbamem.2011.07.022/2 ID: 734 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 303 K (Charmm-Drude, OPENMM 7.5.0, 500 ns) [NMRlipids simulation 734] + name: Molecular dynamics trajectory of a POPC bilayer at 303 K (Charmm-Drude, OPENMM + 7.5.0, 500 ns) [NMRlipids simulation 734] alternateName: 64POPC_6400SOL_303K - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 303 K. Simulated with Charmm-Drude in OPENMM 7.5.0 for 500 ns (56832 atoms). Deposited as NMRlipids Databank simulation 734 and available from https://doi.org/10.5281/zenodo.7607436. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 303 K. Simulated with Charmm-Drude in OPENMM 7.5.0 for 500 ns (56832 atoms). + Deposited as NMRlipids Databank simulation 734 and available from https://doi.org/10.5281/zenodo.7607436. sameAs: https://doi.org/10.5281/zenodo.7607436 datePublished: '2021-03-15' license: @@ -131,7 +134,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.7607436 identifier: 10.5281/zenodo.7607436 url: https://doi.org/10.5281/zenodo.7607436 - name: Pure POPC membrane simulations with the CHARMM-Drude force field (OpenMM 7.5.0) + name: Pure POPC membrane simulations with the CHARMM-Drude force field (OpenMM + 7.5.0) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/e98/55c/e9855c9d36a1dabc244570c99332c1df87333dbe/09332e7c0462dcb58a2d717fd760057c08726706/README.yaml b/Simulations/e98/55c/e9855c9d36a1dabc244570c99332c1df87333dbe/09332e7c0462dcb58a2d717fd760057c08726706/README.yaml index 211bee426d..aed5d1e9fe 100644 --- a/Simulations/e98/55c/e9855c9d36a1dabc244570c99332c1df87333dbe/09332e7c0462dcb58a2d717fd760057c08726706/README.yaml +++ b/Simulations/e98/55c/e9855c9d36a1dabc244570c99332c1df87333dbe/09332e7c0462dcb58a2d717fd760057c08726706/README.yaml @@ -55,9 +55,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 350 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (52:32:16) bilayer at 313 K (ECC-lipids, GROMACS 5.1.4, 300 ns) [NMRlipids simulation 350] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (52:32:16) bilayer at 313 + K (ECC-lipids, GROMACS 5.1.4, 300 ns) [NMRlipids simulation 350] alternateName: 128POPC_6400SOL_40CAL_80CLA_313K_OPC4model - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 52 mol%), 80 CLA (32 mol%) and 40 CAL (16 mol%) at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 300 ns (42872 atoms). Deposited as NMRlipids Databank simulation 350 and available from https://doi.org/10.5281/zenodo.1118980. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 52 mol%), 80 CLA (32 mol%) and 40 CAL (16 mol%) at 313 K. Simulated with ECC-lipids + in GROMACS 5.1.4 for 300 ns (42872 atoms). Deposited as NMRlipids Databank simulation + 350 and available from https://doi.org/10.5281/zenodo.1118980. sameAs: https://doi.org/10.5281/zenodo.1118980 datePublished: '2017-12-19' license: @@ -147,7 +151,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1118980 identifier: 10.5281/zenodo.1118980 url: https://doi.org/10.5281/zenodo.1118980 - name: Simulations Of Popc Lipid Bilayer In Water Solution At Various Nacl And Cacl2 Concentrations Using Ecc-Popc Force Field And Various Water Models + name: Simulations Of Popc Lipid Bilayer In Water Solution At Various Nacl And + Cacl2 Concentrations Using Ecc-Popc Force Field And Various Water Models publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/e9e/979/e9e979c6542306cf52a071c3a7efc2f78818e6d8/694b39c9ad5c9eb43485ea0a2148f0aae3eea22c/README.yaml b/Simulations/e9e/979/e9e979c6542306cf52a071c3a7efc2f78818e6d8/694b39c9ad5c9eb43485ea0a2148f0aae3eea22c/README.yaml index f64facddee..b6df8f3212 100644 --- a/Simulations/e9e/979/e9e979c6542306cf52a071c3a7efc2f78818e6d8/694b39c9ad5c9eb43485ea0a2148f0aae3eea22c/README.yaml +++ b/Simulations/e9e/979/e9e979c6542306cf52a071c3a7efc2f78818e6d8/694b39c9ad5c9eb43485ea0a2148f0aae3eea22c/README.yaml @@ -53,9 +53,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/9 ID: 717 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (53:47) bilayer at 298.15 K (Lipid17, GROMACS 2021, 1001 ns) [NMRlipids simulation 717] + name: Molecular dynamics trajectory of a POPC/CHOL (53:47) bilayer at 298.15 K (Lipid17, + GROMACS 2021, 1001 ns) [NMRlipids simulation 717] alternateName: Lipid17_POPC_CHOL47_L - description: Molecular dynamics trajectory of a lipid bilayer of 1024 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 53 mol%) and 896 CHOL (cholesterol, 47 mol%) at 298.15 K. Simulated with Lipid17 in GROMACS 2021 for 1001 ns (491520 atoms). Deposited as NMRlipids Databank simulation 717 and available from https://doi.org/10.5281/zenodo.6992065. + description: Molecular dynamics trajectory of a lipid bilayer of 1024 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 53 mol%) and 896 CHOL (cholesterol, 47 mol%) at 298.15 K. Simulated with Lipid17 + in GROMACS 2021 for 1001 ns (491520 atoms). Deposited as NMRlipids Databank simulation + 717 and available from https://doi.org/10.5281/zenodo.6992065. sameAs: https://doi.org/10.5281/zenodo.6992065 datePublished: '2022-08-15' license: diff --git a/Simulations/ea0/d5a/ea0d5a1550d15ecabd0ffc0a27f59a7c01f61b83/570401bcf40f667dc9b035d8d5519aeb4a3fa072/README.yaml b/Simulations/ea0/d5a/ea0d5a1550d15ecabd0ffc0a27f59a7c01f61b83/570401bcf40f667dc9b035d8d5519aeb4a3fa072/README.yaml index 4f8f1f4732..1dfb9a57ec 100644 --- a/Simulations/ea0/d5a/ea0d5a1550d15ecabd0ffc0a27f59a7c01f61b83/570401bcf40f667dc9b035d8d5519aeb4a3fa072/README.yaml +++ b/Simulations/ea0/d5a/ea0d5a1550d15ecabd0ffc0a27f59a7c01f61b83/570401bcf40f667dc9b035d8d5519aeb4a3fa072/README.yaml @@ -40,9 +40,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 582 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 298 K (MacRog, GROMACS 4.5.5, 50 ns) [NMRlipids simulation 582] + name: Molecular dynamics trajectory of a POPC bilayer at 298 K (MacRog, GROMACS + 4.5.5, 50 ns) [NMRlipids simulation 582] alternateName: 288POPC_4320SOL_298K - description: Molecular dynamics trajectory of a lipid bilayer of 288 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 298 K. Simulated with MacRog in GROMACS 4.5.5 for 50 ns (51552 atoms). Deposited as NMRlipids Databank simulation 582 and available from https://doi.org/10.5281/zenodo.13498. + description: Molecular dynamics trajectory of a lipid bilayer of 288 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 298 K. Simulated with MacRog in GROMACS 4.5.5 for 50 ns (51552 atoms). Deposited + as NMRlipids Databank simulation 582 and available from https://doi.org/10.5281/zenodo.13498. sameAs: https://doi.org/10.5281/zenodo.13498 datePublished: '2014-12-30' license: diff --git a/Simulations/ea1/4e5/ea14e5e715ff446333e0a1ffc1c7e646fc66ff99/924c07d6e9328d1779f429f3fb80aa27c94d5910/README.yaml b/Simulations/ea1/4e5/ea14e5e715ff446333e0a1ffc1c7e646fc66ff99/924c07d6e9328d1779f429f3fb80aa27c94d5910/README.yaml index 0bf8fc43bd..1eda5940a0 100644 --- a/Simulations/ea1/4e5/ea14e5e715ff446333e0a1ffc1c7e646fc66ff99/924c07d6e9328d1779f429f3fb80aa27c94d5910/README.yaml +++ b/Simulations/ea1/4e5/ea14e5e715ff446333e0a1ffc1c7e646fc66ff99/924c07d6e9328d1779f429f3fb80aa27c94d5910/README.yaml @@ -39,9 +39,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 819 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 314 K (Charmm36, GROMACS 2019.5, 400 ns) [NMRlipids simulation 819] + name: Molecular dynamics trajectory of a POPC bilayer at 314 K (Charmm36, GROMACS + 2019.5, 400 ns) [NMRlipids simulation 819] alternateName: POPС(300K, 20w/l, CHARMM36) - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 314 K. Simulated with Charmm36 in GROMACS 2019.5 for 400 ns (38800 atoms). Deposited as NMRlipids Databank simulation 819 and available from https://doi.org/10.5281/zenodo.6335769. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 314 K. Simulated with Charmm36 in GROMACS 2019.5 for 400 ns (38800 atoms). + Deposited as NMRlipids Databank simulation 819 and available from https://doi.org/10.5281/zenodo.6335769. sameAs: https://doi.org/10.5281/zenodo.6335769 datePublished: '2022-03-07' license: diff --git a/Simulations/ea3/059/ea3059027b7a45871529753525e02e550f45ff6a/7def7dd09d966fd89126e83b919e81267225f35d/README.yaml b/Simulations/ea3/059/ea3059027b7a45871529753525e02e550f45ff6a/7def7dd09d966fd89126e83b919e81267225f35d/README.yaml index 5371102605..6b5b905ddc 100644 --- a/Simulations/ea3/059/ea3059027b7a45871529753525e02e550f45ff6a/7def7dd09d966fd89126e83b919e81267225f35d/README.yaml +++ b/Simulations/ea3/059/ea3059027b7a45871529753525e02e550f45ff6a/7def7dd09d966fd89126e83b919e81267225f35d/README.yaml @@ -49,9 +49,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 143 bioschema_properties: - name: Molecular dynamics trajectory of a POPE/CLA/SOD (83:8:8) bilayer at 310 K (Lipid17, GROMACS 2020.1, 100 ns) [NMRlipids simulation 143] + name: Molecular dynamics trajectory of a POPE/CLA/SOD (83:8:8) bilayer at 310 K + (Lipid17, GROMACS 2020.1, 100 ns) [NMRlipids simulation 143] alternateName: 500POPE_50SOD_50CLA_25000SOL_310K - description: Molecular dynamics trajectory of a lipid bilayer of 500 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 83 mol%), 50 CLA (8 mol%) and 50 SOD (8 mol%) at 310 K. Simulated with Lipid17 in GROMACS 2020.1 for 100 ns (137600 atoms). Deposited as NMRlipids Databank simulation 143 and available from https://doi.org/10.5281/zenodo.4424934. + description: Molecular dynamics trajectory of a lipid bilayer of 500 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, + 83 mol%), 50 CLA (8 mol%) and 50 SOD (8 mol%) at 310 K. Simulated with Lipid17 + in GROMACS 2020.1 for 100 ns (137600 atoms). Deposited as NMRlipids Databank simulation + 143 and available from https://doi.org/10.5281/zenodo.4424934. sameAs: https://doi.org/10.5281/zenodo.4424934 datePublished: '2019-02-25' license: @@ -141,7 +145,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.4424934 identifier: 10.5281/zenodo.4424934 url: https://doi.org/10.5281/zenodo.4424934 - name: LIPID17 POPE Bilayer Simulation (Last 100 ns, 150 mM NaCl, 310 K ) using dihedral 9 + name: LIPID17 POPE Bilayer Simulation (Last 100 ns, 150 mM NaCl, 310 K ) using + dihedral 9 publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/ea5/558/ea5558b751eb04ddecf57ecf511215c695fa6cf6/7821048a45f6b7db4fa1448d6adae485623bf948/README.yaml b/Simulations/ea5/558/ea5558b751eb04ddecf57ecf511215c695fa6cf6/7821048a45f6b7db4fa1448d6adae485623bf948/README.yaml index 848284a280..9920b112a4 100644 --- a/Simulations/ea5/558/ea5558b751eb04ddecf57ecf511215c695fa6cf6/7821048a45f6b7db4fa1448d6adae485623bf948/README.yaml +++ b/Simulations/ea5/558/ea5558b751eb04ddecf57ecf511215c695fa6cf6/7821048a45f6b7db4fa1448d6adae485623bf948/README.yaml @@ -50,9 +50,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 565 bioschema_properties: - name: Molecular dynamics trajectory of a CLA/POPC/CAL (47:30:23) bilayer at 303 K (CHARMM36, GROMACS 5.0.4, 100 ns) [NMRlipids simulation 565] + name: Molecular dynamics trajectory of a CLA/POPC/CAL (47:30:23) bilayer at 303 + K (CHARMM36, GROMACS 5.0.4, 100 ns) [NMRlipids simulation 565] alternateName: 128POPC_6400SOL_100CAL_200CLA_303K - description: Molecular dynamics trajectory of a lipid bilayer of 200 CLA (47 mol%), 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 30 mol%) and 100 CAL (23 mol%) at 303 K. Simulated with CHARMM36 in GROMACS 5.0.4 for 100 ns (36652 atoms). Deposited as NMRlipids Databank simulation 565 and available from https://doi.org/10.5281/zenodo.35156. + description: Molecular dynamics trajectory of a lipid bilayer of 200 CLA (47 mol%), + 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 30 mol%) and 100 CAL + (23 mol%) at 303 K. Simulated with CHARMM36 in GROMACS 5.0.4 for 100 ns (36652 + atoms). Deposited as NMRlipids Databank simulation 565 and available from https://doi.org/10.5281/zenodo.35156. sameAs: https://doi.org/10.5281/zenodo.35156 datePublished: '2015-12-10' license: diff --git a/Simulations/ea5/b83/ea5b83973e55fac3e508449eb0c59c89d48dddcf/02da55bad9f8bb7054f9f5142d9263ef5fd621e1/README.yaml b/Simulations/ea5/b83/ea5b83973e55fac3e508449eb0c59c89d48dddcf/02da55bad9f8bb7054f9f5142d9263ef5fd621e1/README.yaml index 8a1a6926e9..fa52222a60 100644 --- a/Simulations/ea5/b83/ea5b83973e55fac3e508449eb0c59c89d48dddcf/02da55bad9f8bb7054f9f5142d9263ef5fd621e1/README.yaml +++ b/Simulations/ea5/b83/ea5b83973e55fac3e508449eb0c59c89d48dddcf/02da55bad9f8bb7054f9f5142d9263ef5fd621e1/README.yaml @@ -50,9 +50,13 @@ SOFTWARE: gromacs DIR_WRK: /usr/home/bort/Databank ID: 564 bioschema_properties: - name: Molecular dynamics trajectory of a DAPC/CHOL (71:29) bilayer at 310 K (CHARMM36, GROMACS, 1000 ns) [NMRlipids simulation 564] + name: Molecular dynamics trajectory of a DAPC/CHOL (71:29) bilayer at 310 K (CHARMM36, + GROMACS, 1000 ns) [NMRlipids simulation 564] alternateName: 204DAPC_84CHOL_11520SOL_310K - description: Molecular dynamics trajectory of a lipid bilayer of 204 DAPC (1,2-diarachidonoyl-sn-glycero-3-phosphocholine, 71 mol%) and 84 CHOL (cholesterol, 29 mol%) at 310 K. Simulated with CHARMM36 in GROMACS for 1000 ns (68928 atoms). Deposited as NMRlipids Databank simulation 564 and available from https://doi.org/10.5281/zenodo.2653721. + description: Molecular dynamics trajectory of a lipid bilayer of 204 DAPC (1,2-diarachidonoyl-sn-glycero-3-phosphocholine, + 71 mol%) and 84 CHOL (cholesterol, 29 mol%) at 310 K. Simulated with CHARMM36 + in GROMACS for 1000 ns (68928 atoms). Deposited as NMRlipids Databank simulation + 564 and available from https://doi.org/10.5281/zenodo.2653721. sameAs: https://doi.org/10.5281/zenodo.2653721 datePublished: '2019-04-29' license: @@ -141,7 +145,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.2653721 identifier: 10.5281/zenodo.2653721 url: https://doi.org/10.5281/zenodo.2653721 - name: Atomistic simulations of cholesterol in symmetric lipid bilayers with varying degrees of lipid chain unsaturation + name: Atomistic simulations of cholesterol in symmetric lipid bilayers with varying + degrees of lipid chain unsaturation publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/ea8/fd7/ea8fd7ddb853bbb0bf064228dc85e18a95853fc2/26c639faba0c0a3ab0f23cd739b4c764e5d12bcd/README.yaml b/Simulations/ea8/fd7/ea8fd7ddb853bbb0bf064228dc85e18a95853fc2/26c639faba0c0a3ab0f23cd739b4c764e5d12bcd/README.yaml index fa17fde1de..c657a8c80c 100644 --- a/Simulations/ea8/fd7/ea8fd7ddb853bbb0bf064228dc85e18a95853fc2/26c639faba0c0a3ab0f23cd739b4c764e5d12bcd/README.yaml +++ b/Simulations/ea8/fd7/ea8fd7ddb853bbb0bf064228dc85e18a95853fc2/26c639faba0c0a3ab0f23cd739b4c764e5d12bcd/README.yaml @@ -49,9 +49,14 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 71 bioschema_properties: - name: Molecular dynamics trajectory of a SOD/POPG/CLA (50:46:4) bilayer at 310 K (CHARMM36 and CHARMM TIP3P, GROMACS 5.1.2, 100 ns) [NMRlipids simulation 71] + name: Molecular dynamics trajectory of a SOD/POPG/CLA (50:46:4) bilayer at 310 K + (CHARMM36 and CHARMM TIP3P, GROMACS 5.1.2, 100 ns) [NMRlipids simulation 71] alternateName: 500POPG_25000SOL_549SOD_49CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 549 SOD (50 mol%), 500 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 46 mol%) and 49 CLA (4 mol%) at 310 K. Simulated with CHARMM36 and CHARMM TIP3P in GROMACS 5.1.2 for 100 ns (139098 atoms). Deposited as NMRlipids Databank simulation 71 and available from https://doi.org/10.5281/zenodo.2573531. + description: Molecular dynamics trajectory of a lipid bilayer of 549 SOD (50 mol%), + 500 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 46 mol%) and 49 CLA + (4 mol%) at 310 K. Simulated with CHARMM36 and CHARMM TIP3P in GROMACS 5.1.2 for + 100 ns (139098 atoms). Deposited as NMRlipids Databank simulation 71 and available + from https://doi.org/10.5281/zenodo.2573531. sameAs: https://doi.org/10.5281/zenodo.2573531 datePublished: '2019-02-20' license: diff --git a/Simulations/eb4/ab4/eb4ab41fb73a8dfefe1cda75ecc5b036a169f04b/2e9d5a4f3e0a953aa3855e2470ebc83fb0a54dd7/README.yaml b/Simulations/eb4/ab4/eb4ab41fb73a8dfefe1cda75ecc5b036a169f04b/2e9d5a4f3e0a953aa3855e2470ebc83fb0a54dd7/README.yaml index 33e8669c78..6149887941 100644 --- a/Simulations/eb4/ab4/eb4ab41fb73a8dfefe1cda75ecc5b036a169f04b/2e9d5a4f3e0a953aa3855e2470ebc83fb0a54dd7/README.yaml +++ b/Simulations/eb4/ab4/eb4ab41fb73a8dfefe1cda75ecc5b036a169f04b/2e9d5a4f3e0a953aa3855e2470ebc83fb0a54dd7/README.yaml @@ -42,9 +42,12 @@ EXPERIMENT: - 10.1016/j.bbamem.2011.07.022/2 ID: 154 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 303 K (Lipid14, GROMACS 4.5, 50 ns) [NMRlipids simulation 154] + name: Molecular dynamics trajectory of a POPC bilayer at 303 K (Lipid14, GROMACS + 4.5, 50 ns) [NMRlipids simulation 154] alternateName: 72POPC_2234SOL_303K - description: Molecular dynamics trajectory of a lipid bilayer of 72 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 303 K. Simulated with Lipid14 in GROMACS 4.5 for 50 ns (16350 atoms). Deposited as NMRlipids Databank simulation 154 and available from https://doi.org/10.5281/zenodo.12767. + description: Molecular dynamics trajectory of a lipid bilayer of 72 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 303 K. Simulated with Lipid14 in GROMACS 4.5 for 50 ns (16350 atoms). Deposited + as NMRlipids Databank simulation 154 and available from https://doi.org/10.5281/zenodo.12767. sameAs: https://doi.org/10.5281/zenodo.12767 datePublished: '2014-11-19' license: @@ -133,7 +136,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.12767 identifier: 10.5281/zenodo.12767 url: https://doi.org/10.5281/zenodo.12767 - name: Md Simulation Trajectory And Related Files For Popc Bilayer (Lipid14, Gromacs 4.5) + name: Md Simulation Trajectory And Related Files For Popc Bilayer (Lipid14, Gromacs + 4.5) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/eba/d7b/ebad7bde0e3d5e5fcc3a64387f569e10162fe7c0/9caac3eaf3998263deea32cbee2b2f947d38dcea/README.yaml b/Simulations/eba/d7b/ebad7bde0e3d5e5fcc3a64387f569e10162fe7c0/9caac3eaf3998263deea32cbee2b2f947d38dcea/README.yaml index 6264deaee8..341fc35885 100644 --- a/Simulations/eba/d7b/ebad7bde0e3d5e5fcc3a64387f569e10162fe7c0/9caac3eaf3998263deea32cbee2b2f947d38dcea/README.yaml +++ b/Simulations/eba/d7b/ebad7bde0e3d5e5fcc3a64387f569e10162fe7c0/9caac3eaf3998263deea32cbee2b2f947d38dcea/README.yaml @@ -44,9 +44,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/1 ID: 30 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 298.15 K (Lipid14 with Verlet scheme, GROMACS 5.0.3, 100 ns) [NMRlipids simulation 30] + name: Molecular dynamics trajectory of a POPC bilayer at 298.15 K (Lipid14 with + Verlet scheme, GROMACS 5.0.3, 100 ns) [NMRlipids simulation 30] alternateName: 128POPC_5120SOL_298K - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 298.15 K. Simulated with Lipid14 with Verlet scheme in GROMACS 5.0.3 for 100 ns (32512 atoms). Deposited as NMRlipids Databank simulation 30 and available from https://doi.org/10.5281/zenodo.30898. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 298.15 K. Simulated with Lipid14 with Verlet scheme in GROMACS 5.0.3 for 100 + ns (32512 atoms). Deposited as NMRlipids Databank simulation 30 and available + from https://doi.org/10.5281/zenodo.30898. sameAs: https://doi.org/10.5281/zenodo.30898 datePublished: '2015-09-11' license: diff --git a/Simulations/ebb/ca8/ebbca82ace6baca0eba4d8e154196c49dddef206/bd232347e593006376a2344ec2e97ffa5655f20c/README.yaml b/Simulations/ebb/ca8/ebbca82ace6baca0eba4d8e154196c49dddef206/bd232347e593006376a2344ec2e97ffa5655f20c/README.yaml index 8cdafb6d21..268341eeb4 100644 --- a/Simulations/ebb/ca8/ebbca82ace6baca0eba4d8e154196c49dddef206/bd232347e593006376a2344ec2e97ffa5655f20c/README.yaml +++ b/Simulations/ebb/ca8/ebbca82ace6baca0eba4d8e154196c49dddef206/bd232347e593006376a2344ec2e97ffa5655f20c/README.yaml @@ -57,9 +57,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 211 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL/CLA/SOD (76:8:8:8) bilayer at 310 K (Slipids for lipids and Smith & Dang for ions, GROMACS 4.6, 200 ns) [NMRlipids simulation 211] + name: Molecular dynamics trajectory of a POPC/CHOL/CLA/SOD (76:8:8:8) bilayer at + 310 K (Slipids for lipids and Smith & Dang for ions, GROMACS 4.6, 200 ns) [NMRlipids + simulation 211] alternateName: 22CHOL_200POPC_9000SOL_21SOD_21CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 76 mol%), 22 CHOL (cholesterol, 8 mol%), 21 CLA (8 mol%) and 21 SOD (8 mol%) at 310 K. Simulated with Slipids for lipids and Smith & Dang for ions in GROMACS 4.6 for 200 ns (55470 atoms). Deposited as NMRlipids Databank simulation 211 and available from https://doi.org/10.5281/zenodo.259335. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 76 mol%), 22 CHOL (cholesterol, 8 mol%), 21 CLA (8 mol%) and 21 SOD (8 mol%) at + 310 K. Simulated with Slipids for lipids and Smith & Dang for ions in GROMACS + 4.6 for 200 ns (55470 atoms). Deposited as NMRlipids Databank simulation 211 and + available from https://doi.org/10.5281/zenodo.259335. sameAs: https://doi.org/10.5281/zenodo.259335 datePublished: '2017-01-24' license: @@ -149,7 +155,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.259335 identifier: 10.5281/zenodo.259335 url: https://doi.org/10.5281/zenodo.259335 - name: Popc With Varying Amounts Of Cholesterol, 130 Mm Of Nacl. Slipids With Ions By Smith & Dang + name: Popc With Varying Amounts Of Cholesterol, 130 Mm Of Nacl. Slipids With Ions + By Smith & Dang publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/ec5/c0c/ec5c0c97103fc266077f877851c4f47162362674/c82e638566fbc5cc49783178bfaafc01fc72bf5f/README.yaml b/Simulations/ec5/c0c/ec5c0c97103fc266077f877851c4f47162362674/c82e638566fbc5cc49783178bfaafc01fc72bf5f/README.yaml index 9bd4f12f15..282c859530 100644 --- a/Simulations/ec5/c0c/ec5c0c97103fc266077f877851c4f47162362674/c82e638566fbc5cc49783178bfaafc01fc72bf5f/README.yaml +++ b/Simulations/ec5/c0c/ec5c0c97103fc266077f877851c4f47162362674/c82e638566fbc5cc49783178bfaafc01fc72bf5f/README.yaml @@ -44,9 +44,12 @@ EXPERIMENT: - 10.1021/acs.jpcb.4c04719/1 FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 300 K (OPLS3e, GROMACS Desmond 2019-4, 600 ns) [NMRlipids simulation 796] + name: Molecular dynamics trajectory of a POPC bilayer at 300 K (OPLS3e, GROMACS + Desmond 2019-4, 600 ns) [NMRlipids simulation 796] alternateName: POPС(300K, 5w/l, OPLS3e) - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 300 K. Simulated with OPLS3e in GROMACS Desmond 2019-4 for 600 ns (29800 atoms). Deposited as NMRlipids Databank simulation 796 and available from https://doi.org/10.5281/zenodo.10184229. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 300 K. Simulated with OPLS3e in GROMACS Desmond 2019-4 for 600 ns (29800 atoms). + Deposited as NMRlipids Databank simulation 796 and available from https://doi.org/10.5281/zenodo.10184229. sameAs: https://doi.org/10.5281/zenodo.10184229 datePublished: '2022' license: diff --git a/Simulations/ed4/076/ed4076a232ce5d87dc4a244164604a0b91d9d877/25731b859c4bc2652de35ead4f799ac1d922df28/README.yaml b/Simulations/ed4/076/ed4076a232ce5d87dc4a244164604a0b91d9d877/25731b859c4bc2652de35ead4f799ac1d922df28/README.yaml index 8cf1473900..8e64fd353e 100644 --- a/Simulations/ed4/076/ed4076a232ce5d87dc4a244164604a0b91d9d877/25731b859c4bc2652de35ead4f799ac1d922df28/README.yaml +++ b/Simulations/ed4/076/ed4076a232ce5d87dc4a244164604a0b91d9d877/25731b859c4bc2652de35ead4f799ac1d922df28/README.yaml @@ -55,9 +55,13 @@ DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 382 AUTHORS_CONTACT: Ollila, O. H. Samuli bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/DHMDMAB (81:10:10) bilayer at 313 K (CHARMM36, GROMACS, 200 ns) [NMRlipids simulation 382] + name: Molecular dynamics trajectory of a POPC/CLA/DHMDMAB (81:10:10) bilayer at + 313 K (CHARMM36, GROMACS, 200 ns) [NMRlipids simulation 382] alternateName: POPC10%DHMDMAB_T313K - description: Molecular dynamics trajectory of a lipid bilayer of 100 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 81 mol%), 12 CLA (10 mol%) and 12 DHMDMAB (dihexadecyldimethylammonium, 10 mol%) at 313 K. Simulated with CHARMM36 in GROMACS for 200 ns (38594 atoms). Deposited as NMRlipids Databank simulation 382 and available from https://doi.org/10.5281/zenodo.1288297. + description: Molecular dynamics trajectory of a lipid bilayer of 100 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 81 mol%), 12 CLA (10 mol%) and 12 DHMDMAB (dihexadecyldimethylammonium, 10 mol%) + at 313 K. Simulated with CHARMM36 in GROMACS for 200 ns (38594 atoms). Deposited + as NMRlipids Databank simulation 382 and available from https://doi.org/10.5281/zenodo.1288297. sameAs: https://doi.org/10.5281/zenodo.1288297 datePublished: '2018-06-13' license: diff --git a/Simulations/ede/d7e/eded7ed13c37c4bd48c9a54311bf6d8d06e84a45/7aea0e32c53c370eb8e02dc5ec744153f00c63d5/README.yaml b/Simulations/ede/d7e/eded7ed13c37c4bd48c9a54311bf6d8d06e84a45/7aea0e32c53c370eb8e02dc5ec744153f00c63d5/README.yaml index 10b39df5f4..1c4709be3a 100644 --- a/Simulations/ede/d7e/eded7ed13c37c4bd48c9a54311bf6d8d06e84a45/7aea0e32c53c370eb8e02dc5ec744153f00c63d5/README.yaml +++ b/Simulations/ede/d7e/eded7ed13c37c4bd48c9a54311bf6d8d06e84a45/7aea0e32c53c370eb8e02dc5ec744153f00c63d5/README.yaml @@ -38,9 +38,12 @@ EXPERIMENT: FORMFACTOR: - 10.1016/j.bbamem.2011.07.022/8 bioschema_properties: - name: Molecular dynamics trajectory of a DLPC bilayer at 323 K (CHARMM36/LJ-PME, GROMACS Gromacs 2022, 100 ns) [NMRlipids simulation 918] + name: Molecular dynamics trajectory of a DLPC bilayer at 323 K (CHARMM36/LJ-PME, + GROMACS Gromacs 2022, 100 ns) [NMRlipids simulation 918] alternateName: Fully hydrated DLPC bilayer in SPC/E water (LJ_cutoff=1.2 nm) - description: Molecular dynamics trajectory of a lipid bilayer of 100 DLPC (1,2-dilauroyl-sn-glycero-3-phosphocholine) at 323 K. Simulated with CHARMM36/LJ-PME in GROMACS Gromacs 2022 for 100 ns (23542 atoms). Deposited as NMRlipids Databank simulation 918 and available from https://doi.org/10.5281/zenodo.20579050. + description: Molecular dynamics trajectory of a lipid bilayer of 100 DLPC (1,2-dilauroyl-sn-glycero-3-phosphocholine) + at 323 K. Simulated with CHARMM36/LJ-PME in GROMACS Gromacs 2022 for 100 ns (23542 + atoms). Deposited as NMRlipids Databank simulation 918 and available from https://doi.org/10.5281/zenodo.20579050. sameAs: https://doi.org/10.5281/zenodo.20579050 datePublished: '2026-06-07' license: @@ -131,7 +134,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.20579050 identifier: 10.5281/zenodo.20579050 url: https://doi.org/10.5281/zenodo.20579050 - name: Fully hydrated DLPC bilayer at different temperatures simulated using CHARMM36 with LJ-PME and LJ-cutoff + name: Fully hydrated DLPC bilayer at different temperatures simulated using CHARMM36 + with LJ-PME and LJ-cutoff publisher: Zenodo _source: api: datacite diff --git a/Simulations/edf/8a8/edf8a82ed02a87f84c14b740c90dfa718d3f7f8b/1048c4444299bb5adb360e7e17df2b616ab7a4fc/README.yaml b/Simulations/edf/8a8/edf8a82ed02a87f84c14b740c90dfa718d3f7f8b/1048c4444299bb5adb360e7e17df2b616ab7a4fc/README.yaml index 9e659ee2fc..e72f1906c9 100644 --- a/Simulations/edf/8a8/edf8a82ed02a87f84c14b740c90dfa718d3f7f8b/1048c4444299bb5adb360e7e17df2b616ab7a4fc/README.yaml +++ b/Simulations/edf/8a8/edf8a82ed02a87f84c14b740c90dfa718d3f7f8b/1048c4444299bb5adb360e7e17df2b616ab7a4fc/README.yaml @@ -44,9 +44,12 @@ SOD: NA TRJLENGTH: 150700.0 ID: 612 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 303 K (CHARMM36, GROMACS, 151 ns) [NMRlipids simulation 612] + name: Molecular dynamics trajectory of a POPC bilayer at 303 K (CHARMM36, GROMACS, + 151 ns) [NMRlipids simulation 612] alternateName: POPC_T303K - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 303 K. Simulated with CHARMM36 in GROMACS for 151 ns (32512 atoms). Deposited as NMRlipids Databank simulation 612 and available from https://doi.org/10.5281/zenodo.14066. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 303 K. Simulated with CHARMM36 in GROMACS for 151 ns (32512 atoms). Deposited + as NMRlipids Databank simulation 612 and available from https://doi.org/10.5281/zenodo.14066. sameAs: https://doi.org/10.5281/zenodo.14066 datePublished: '2015-01-19' license: @@ -133,7 +136,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.14066 identifier: 10.5281/zenodo.14066 url: https://doi.org/10.5281/zenodo.14066 - name: Md Simulation Trajectory And Related Files For Popc Bilayer (Charmm36, Gromacs 4.5) + name: Md Simulation Trajectory And Related Files For Popc Bilayer (Charmm36, Gromacs + 4.5) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/ee1/42d/ee142d0421a96d37ea69595cc6f59417c1da5fc6/959016d5e777e7f5c2b0c8fec10f08e3f99d88a1/README.yaml b/Simulations/ee1/42d/ee142d0421a96d37ea69595cc6f59417c1da5fc6/959016d5e777e7f5c2b0c8fec10f08e3f99d88a1/README.yaml index 3db30cad70..149026253c 100644 --- a/Simulations/ee1/42d/ee142d0421a96d37ea69595cc6f59417c1da5fc6/959016d5e777e7f5c2b0c8fec10f08e3f99d88a1/README.yaml +++ b/Simulations/ee1/42d/ee142d0421a96d37ea69595cc6f59417c1da5fc6/959016d5e777e7f5c2b0c8fec10f08e3f99d88a1/README.yaml @@ -63,9 +63,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 241 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CAL/POPS/CLA (62:14:14:10) bilayer at 310 K (Berger, GROMACS 4.5.5, 100 ns) [NMRlipids simulation 241] + name: Molecular dynamics trajectory of a POPC/CAL/POPS/CLA (62:14:14:10) bilayer + at 310 K (Berger, GROMACS 4.5.5, 100 ns) [NMRlipids simulation 241] alternateName: 104POPC_24OPS_4306SOL_24CAL_16CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 104 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 62 mol%), 24 CAL (14 mol%), 24 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 14 mol%) and 16 CLA (10 mol%) at 310 K. Simulated with Berger in GROMACS 4.5.5 for 100 ns (19686 atoms). Deposited as NMRlipids Databank simulation 241 and available from https://doi.org/10.5281/zenodo.887398. + description: Molecular dynamics trajectory of a lipid bilayer of 104 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 62 mol%), 24 CAL (14 mol%), 24 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, + 14 mol%) and 16 CLA (10 mol%) at 310 K. Simulated with Berger in GROMACS 4.5.5 + for 100 ns (19686 atoms). Deposited as NMRlipids Databank simulation 241 and available + from https://doi.org/10.5281/zenodo.887398. sameAs: https://doi.org/10.5281/zenodo.887398 datePublished: '2017-09-07' license: @@ -158,7 +163,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.887398 identifier: 10.5281/zenodo.887398 url: https://doi.org/10.5281/zenodo.887398 - name: Md Simulation Trajectory Of A Popc/Pops (4:1) Bilayer With 102Mm Cacl2, Berger Force Field For Lipids, Scaled Charges For Ca2+ And Cl- + name: Md Simulation Trajectory Of A Popc/Pops (4:1) Bilayer With 102Mm Cacl2, + Berger Force Field For Lipids, Scaled Charges For Ca2+ And Cl- publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/ee1/dda/ee1ddaaac56cb771f423e85475426c11f443fb56/3ea6d1c727116cc8c5f59fc64ce163b83c7b7380/README.yaml b/Simulations/ee1/dda/ee1ddaaac56cb771f423e85475426c11f443fb56/3ea6d1c727116cc8c5f59fc64ce163b83c7b7380/README.yaml index 004579cdda..6f15f8ac66 100644 --- a/Simulations/ee1/dda/ee1ddaaac56cb771f423e85475426c11f443fb56/3ea6d1c727116cc8c5f59fc64ce163b83c7b7380/README.yaml +++ b/Simulations/ee1/dda/ee1ddaaac56cb771f423e85475426c11f443fb56/3ea6d1c727116cc8c5f59fc64ce163b83c7b7380/README.yaml @@ -50,9 +50,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 242 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (39:31:31) bilayer at 310.15 K (CHARMM36, GROMACS, 376 ns) [NMRlipids simulation 242] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (39:31:31) bilayer at 310.15 + K (CHARMM36, GROMACS, 376 ns) [NMRlipids simulation 242] alternateName: 200POPC_9000SOL_157SOD_157CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 39 mol%), 157 CLA (31 mol%) and 157 SOD (31 mol%) at 310.15 K. Simulated with CHARMM36 in GROMACS for 376 ns (54114 atoms). Deposited as NMRlipids Databank simulation 242 and available from https://doi.org/10.5281/zenodo.3434396. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 39 mol%), 157 CLA (31 mol%) and 157 SOD (31 mol%) at 310.15 K. Simulated with + CHARMM36 in GROMACS for 376 ns (54114 atoms). Deposited as NMRlipids Databank + simulation 242 and available from https://doi.org/10.5281/zenodo.3434396. sameAs: https://doi.org/10.5281/zenodo.3434396 datePublished: '2019-09-17' license: diff --git a/Simulations/eec/b7f/eecb7fdab1021ea357d3bdab891fe0db9ada1fd0/b6b0eac9c0091180ea5bc15ca0322ac0c3055bc2/README.yaml b/Simulations/eec/b7f/eecb7fdab1021ea357d3bdab891fe0db9ada1fd0/b6b0eac9c0091180ea5bc15ca0322ac0c3055bc2/README.yaml index 2b2b6d3374..8d2e909cbe 100644 --- a/Simulations/eec/b7f/eecb7fdab1021ea357d3bdab891fe0db9ada1fd0/b6b0eac9c0091180ea5bc15ca0322ac0c3055bc2/README.yaml +++ b/Simulations/eec/b7f/eecb7fdab1021ea357d3bdab891fe0db9ada1fd0/b6b0eac9c0091180ea5bc15ca0322ac0c3055bc2/README.yaml @@ -44,9 +44,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 532 bioschema_properties: - name: Molecular dynamics trajectory of a DOPC bilayer at 293.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 532] + name: Molecular dynamics trajectory of a DOPC bilayer at 293.15 K (CHARMM36, GROMACS, + 1001 ns) [NMRlipids simulation 532] alternateName: 256DOPC_12800SOL_293K - description: Molecular dynamics trajectory of a lipid bilayer of 256 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) at 293.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (73728 atoms). Deposited as NMRlipids Databank simulation 532 and available from https://doi.org/10.5281/zenodo.6943086. + description: Molecular dynamics trajectory of a lipid bilayer of 256 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) + at 293.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (73728 atoms). Deposited + as NMRlipids Databank simulation 532 and available from https://doi.org/10.5281/zenodo.6943086. sameAs: https://doi.org/10.5281/zenodo.6943086 datePublished: '2022-07-30' license: diff --git a/Simulations/ef2/864/ef2864a8cddd413e691097666c509fd0a026ceef/ca9f58f7e48ae3d72fcf96db9951cc6f97f211e5/README.yaml b/Simulations/ef2/864/ef2864a8cddd413e691097666c509fd0a026ceef/ca9f58f7e48ae3d72fcf96db9951cc6f97f211e5/README.yaml index 1ff81210ba..a5617f1e54 100644 --- a/Simulations/ef2/864/ef2864a8cddd413e691097666c509fd0a026ceef/ca9f58f7e48ae3d72fcf96db9951cc6f97f211e5/README.yaml +++ b/Simulations/ef2/864/ef2864a8cddd413e691097666c509fd0a026ceef/ca9f58f7e48ae3d72fcf96db9951cc6f97f211e5/README.yaml @@ -48,9 +48,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 864 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (68:22:11) bilayer at 300 K (OPLS3e, GROMACS Desmond of Schrödinger 2019-4, 1 ns) [NMRlipids simulation 864] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (68:22:11) bilayer at 300 + K (OPLS3e, GROMACS Desmond of Schrödinger 2019-4, 1 ns) [NMRlipids simulation + 864] alternateName: POPC, 44 w/l, 300 K, 0.2 M CaCl2 - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 68 mol%), 64 CLA (22 mol%) and 32 CAL (11 mol%) at 300 K. Simulated with OPLS3e in GROMACS Desmond of Schrödinger 2019-4 for 1 ns (53536 atoms). Deposited as NMRlipids Databank simulation 864 and available from https://doi.org/10.5281/zenodo.6618953. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 68 mol%), 64 CLA (22 mol%) and 32 CAL (11 mol%) at 300 K. Simulated with OPLS3e + in GROMACS Desmond of Schrödinger 2019-4 for 1 ns (53536 atoms). Deposited as + NMRlipids Databank simulation 864 and available from https://doi.org/10.5281/zenodo.6618953. sameAs: https://doi.org/10.5281/zenodo.6618953 datePublished: '2022-03-12' license: @@ -141,7 +146,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.6618953 identifier: 10.5281/zenodo.6618953 url: https://doi.org/10.5281/zenodo.6618953 - name: MD simulation of POPC bilayer with OPLS3e force field, 200 mM CaCl2 part 1 + name: MD simulation of POPC bilayer with OPLS3e force field, 200 mM CaCl2 part + 1 publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/ef4/41c/ef441c853176fefb8f790026dc4473d80fbf8e61/3bd4758d5cad57a8bcbdaf35265550dd7fc0c01a/README.yaml b/Simulations/ef4/41c/ef441c853176fefb8f790026dc4473d80fbf8e61/3bd4758d5cad57a8bcbdaf35265550dd7fc0c01a/README.yaml index bb8cb11aef..cd56555813 100644 --- a/Simulations/ef4/41c/ef441c853176fefb8f790026dc4473d80fbf8e61/3bd4758d5cad57a8bcbdaf35265550dd7fc0c01a/README.yaml +++ b/Simulations/ef4/41c/ef441c853176fefb8f790026dc4473d80fbf8e61/3bd4758d5cad57a8bcbdaf35265550dd7fc0c01a/README.yaml @@ -49,9 +49,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 66 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (84:8:8) bilayer at 310 K (CHARMM36 and CHARMM TIP3P, GROMACS 5.1.2, 100 ns) [NMRlipids simulation 66] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (84:8:8) bilayer at 310 K + (CHARMM36 and CHARMM TIP3P, GROMACS 5.1.2, 100 ns) [NMRlipids simulation 66] alternateName: 500POPC_25000SOL_48SOD_48CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 500 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 84 mol%), 48 CLA (8 mol%) and 48 SOD (8 mol%) at 310 K. Simulated with CHARMM36 and CHARMM TIP3P in GROMACS 5.1.2 for 100 ns (142096 atoms). Deposited as NMRlipids Databank simulation 66 and available from https://doi.org/10.5281/zenodo.2628335. + description: Molecular dynamics trajectory of a lipid bilayer of 500 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 84 mol%), 48 CLA (8 mol%) and 48 SOD (8 mol%) at 310 K. Simulated with CHARMM36 + and CHARMM TIP3P in GROMACS 5.1.2 for 100 ns (142096 atoms). Deposited as NMRlipids + Databank simulation 66 and available from https://doi.org/10.5281/zenodo.2628335. sameAs: https://doi.org/10.5281/zenodo.2628335 datePublished: '2019-02-25' license: diff --git a/Simulations/ef4/520/ef45203f9f3dec57f2dcffb6fee9b51fe9447f08/ef45203f9f3dec57f2dcffb6fee9b51fe9447f08/README.yaml b/Simulations/ef4/520/ef45203f9f3dec57f2dcffb6fee9b51fe9447f08/ef45203f9f3dec57f2dcffb6fee9b51fe9447f08/README.yaml index 71e4846a97..0020bcfc20 100644 --- a/Simulations/ef4/520/ef45203f9f3dec57f2dcffb6fee9b51fe9447f08/ef45203f9f3dec57f2dcffb6fee9b51fe9447f08/README.yaml +++ b/Simulations/ef4/520/ef45203f9f3dec57f2dcffb6fee9b51fe9447f08/ef45203f9f3dec57f2dcffb6fee9b51fe9447f08/README.yaml @@ -42,9 +42,12 @@ EXPERIMENT: FORMFACTOR: - 10.1021/jp511159q/1 bioschema_properties: - name: Molecular dynamics trajectory of a POPE bilayer at 308 K (Charmm-Drude polarizable, OPENMM, 200 ns) [NMRlipids simulation 747] + name: Molecular dynamics trajectory of a POPE bilayer at 308 K (Charmm-Drude polarizable, + OPENMM, 200 ns) [NMRlipids simulation 747] alternateName: POPE_CHARMMdrude2023_308K - description: Molecular dynamics trajectory of a lipid bilayer of 72 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) at 308 K. Simulated with Charmm-Drude polarizable in OPENMM for 200 ns (24624 atoms). Deposited as NMRlipids Databank simulation 747 and available from https://doi.org/10.5281/zenodo.7916494. + description: Molecular dynamics trajectory of a lipid bilayer of 72 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) + at 308 K. Simulated with Charmm-Drude polarizable in OPENMM for 200 ns (24624 + atoms). Deposited as NMRlipids Databank simulation 747 and available from https://doi.org/10.5281/zenodo.7916494. sameAs: https://doi.org/10.5281/zenodo.7916494 datePublished: '2023-05-09' license: @@ -134,7 +137,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.7916494 identifier: 10.5281/zenodo.7916494 url: https://doi.org/10.5281/zenodo.7916494 - name: OpenMM simulations of POPE using the CHARMM Drude2023 force field in xtc format + name: OpenMM simulations of POPE using the CHARMM Drude2023 force field in xtc + format publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/efe/f45/efef45ac201347d6822e5436d2566d3be298b54a/a2c7ff5a30728119cc82206b15a3df9fb63eaf5e/README.yaml b/Simulations/efe/f45/efef45ac201347d6822e5436d2566d3be298b54a/a2c7ff5a30728119cc82206b15a3df9fb63eaf5e/README.yaml index 376dfd0021..7a5f367a56 100644 --- a/Simulations/efe/f45/efef45ac201347d6822e5436d2566d3be298b54a/a2c7ff5a30728119cc82206b15a3df9fb63eaf5e/README.yaml +++ b/Simulations/efe/f45/efef45ac201347d6822e5436d2566d3be298b54a/a2c7ff5a30728119cc82206b15a3df9fb63eaf5e/README.yaml @@ -56,9 +56,14 @@ TRJ: TEMPERATURE: 298.0 ID: 417 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/POPG/SOD/CAL (52:14:13:13:7) bilayer at 298 K (lipid17ecc, GROMACS, 300 ns) [NMRlipids simulation 417] + name: Molecular dynamics trajectory of a POPC/CLA/POPG/SOD/CAL (52:14:13:13:7) bilayer + at 298 K (lipid17ecc, GROMACS, 300 ns) [NMRlipids simulation 417] alternateName: POPC:POPG(4:1)_T298K_0.1MCaCl - description: Molecular dynamics trajectory of a lipid bilayer of 350 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 52 mol%), 94 CLA (14 mol%), 88 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 13 mol%), 88 SOD (13 mol%) and 47 CAL (7 mol%) at 298 K. Simulated with lipid17ecc in GROMACS for 300 ns (136677 atoms). Deposited as NMRlipids Databank simulation 417 and available from https://doi.org/10.5281/zenodo.3997176. + description: Molecular dynamics trajectory of a lipid bilayer of 350 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 52 mol%), 94 CLA (14 mol%), 88 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, + 13 mol%), 88 SOD (13 mol%) and 47 CAL (7 mol%) at 298 K. Simulated with lipid17ecc + in GROMACS for 300 ns (136677 atoms). Deposited as NMRlipids Databank simulation + 417 and available from https://doi.org/10.5281/zenodo.3997176. sameAs: https://doi.org/10.5281/zenodo.3997176 datePublished: '2020-08-24' license: @@ -148,7 +153,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3997176 identifier: 10.5281/zenodo.3997176 url: https://doi.org/10.5281/zenodo.3997176 - name: Lipid17ecc POPC:POPG 4:1 bilayer simulation in 0.1 M CaCl2 solution and Na+ counter ions + name: Lipid17ecc POPC:POPG 4:1 bilayer simulation in 0.1 M CaCl2 solution and + Na+ counter ions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/f02/6fb/f026fbc2272c63e20d187ae3ff06d24c69a7034e/eec18f57040147ff6fe48691622ac000a9fb365c/README.yaml b/Simulations/f02/6fb/f026fbc2272c63e20d187ae3ff06d24c69a7034e/eec18f57040147ff6fe48691622ac000a9fb365c/README.yaml index 8458e06f6a..6ff1d416e3 100644 --- a/Simulations/f02/6fb/f026fbc2272c63e20d187ae3ff06d24c69a7034e/eec18f57040147ff6fe48691622ac000a9fb365c/README.yaml +++ b/Simulations/f02/6fb/f026fbc2272c63e20d187ae3ff06d24c69a7034e/eec18f57040147ff6fe48691622ac000a9fb365c/README.yaml @@ -49,9 +49,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 50 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (83:9:9) bilayer at 310 K (Slipids for lipids, Smith and Dang for NaCl, GROMACS 4.6, 100 ns) [NMRlipids simulation 50] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (83:9:9) bilayer at 310 K + (Slipids for lipids, Smith and Dang for NaCl, GROMACS 4.6, 100 ns) [NMRlipids + simulation 50] alternateName: 200POPC_9000SOL_21SOD_21CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 83 mol%), 21 CLA (9 mol%) and 21 SOD (9 mol%) at 310 K. Simulated with Slipids for lipids, Smith and Dang for NaCl in GROMACS 4.6 for 100 ns (53842 atoms). Deposited as NMRlipids Databank simulation 50 and available from https://doi.org/10.5281/zenodo.35275. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 83 mol%), 21 CLA (9 mol%) and 21 SOD (9 mol%) at 310 K. Simulated with Slipids + for lipids, Smith and Dang for NaCl in GROMACS 4.6 for 100 ns (53842 atoms). Deposited + as NMRlipids Databank simulation 50 and available from https://doi.org/10.5281/zenodo.35275. sameAs: https://doi.org/10.5281/zenodo.35275 datePublished: '2015-12-12' license: diff --git a/Simulations/f07/1aa/f071aa10d13d9eca665430308082317769f4172e/22e6c3544690d4405b6933bf77972a73009ae9ac/README.yaml b/Simulations/f07/1aa/f071aa10d13d9eca665430308082317769f4172e/22e6c3544690d4405b6933bf77972a73009ae9ac/README.yaml index d5a03b7697..c0cdfd78ab 100644 --- a/Simulations/f07/1aa/f071aa10d13d9eca665430308082317769f4172e/22e6c3544690d4405b6933bf77972a73009ae9ac/README.yaml +++ b/Simulations/f07/1aa/f071aa10d13d9eca665430308082317769f4172e/22e6c3544690d4405b6933bf77972a73009ae9ac/README.yaml @@ -44,9 +44,12 @@ EXPERIMENT: FORMFACTOR: - 10.1016/j.bbamem.2011.07.022/18 bioschema_properties: - name: Molecular dynamics trajectory of a DMPC bilayer at 303.15 K (Lipid21(AMBER), GROMACS 2026.1, 100 ns) [NMRlipids simulation 912] + name: Molecular dynamics trajectory of a DMPC bilayer at 303.15 K (Lipid21(AMBER), + GROMACS 2026.1, 100 ns) [NMRlipids simulation 912] alternateName: DMPC - description: Molecular dynamics trajectory of a lipid bilayer of 40 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) at 303.15 K. Simulated with Lipid21(AMBER) in GROMACS 2026.1 for 100 ns (8800 atoms). Deposited as NMRlipids Databank simulation 912 and available from https://doi.org/10.5281/zenodo.20558593. + description: Molecular dynamics trajectory of a lipid bilayer of 40 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) + at 303.15 K. Simulated with Lipid21(AMBER) in GROMACS 2026.1 for 100 ns (8800 + atoms). Deposited as NMRlipids Databank simulation 912 and available from https://doi.org/10.5281/zenodo.20558593. sameAs: https://doi.org/10.5281/zenodo.20558593 datePublished: '2026-06-07' license: @@ -140,7 +143,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.20558593 identifier: 10.5281/zenodo.20558593 url: https://doi.org/10.5281/zenodo.20558593 - name: MD simulation trajectory and related files for DMPC lipid bilayer in full hydration at 303 K with Lipid21 + name: MD simulation trajectory and related files for DMPC lipid bilayer in full + hydration at 303 K with Lipid21 publisher: Zenodo _source: api: datacite diff --git a/Simulations/f0d/4e1/f0d4e124ce03150e4b699e734c162ac90913a5cc/68992b2eaf729ba5ea8090b722f27509e2b174c7/README.yaml b/Simulations/f0d/4e1/f0d4e124ce03150e4b699e734c162ac90913a5cc/68992b2eaf729ba5ea8090b722f27509e2b174c7/README.yaml index c1990972e3..b358030060 100644 --- a/Simulations/f0d/4e1/f0d4e124ce03150e4b699e734c162ac90913a5cc/68992b2eaf729ba5ea8090b722f27509e2b174c7/README.yaml +++ b/Simulations/f0d/4e1/f0d4e124ce03150e4b699e734c162ac90913a5cc/68992b2eaf729ba5ea8090b722f27509e2b174c7/README.yaml @@ -51,9 +51,13 @@ EXPERIMENT: CHOL: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a DOPC/CHOL (89:11) bilayer at 333.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 647] + name: Molecular dynamics trajectory of a DOPC/CHOL (89:11) bilayer at 333.15 K (CHARMM36, + GROMACS, 1001 ns) [NMRlipids simulation 647] alternateName: 256DOPC_32CHOL_14400SOL_333K - description: Molecular dynamics trajectory of a lipid bilayer of 256 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, 89 mol%) and 32 CHOL (cholesterol, 11 mol%) at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (80896 atoms). Deposited as NMRlipids Databank simulation 647 and available from https://doi.org/10.5281/zenodo.6943929. + description: Molecular dynamics trajectory of a lipid bilayer of 256 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, + 89 mol%) and 32 CHOL (cholesterol, 11 mol%) at 333.15 K. Simulated with CHARMM36 + in GROMACS for 1001 ns (80896 atoms). Deposited as NMRlipids Databank simulation + 647 and available from https://doi.org/10.5281/zenodo.6943929. sameAs: https://doi.org/10.5281/zenodo.6943929 datePublished: '2022-07-30' license: diff --git a/Simulations/f15/031/f15031b9680ce3490833380d4a94f40a270fb89f/75ff31fe588d7d0b2f330a693cba4f99c7ebef05/README.yaml b/Simulations/f15/031/f15031b9680ce3490833380d4a94f40a270fb89f/75ff31fe588d7d0b2f330a693cba4f99c7ebef05/README.yaml index 50f8492b26..1b8078edc1 100644 --- a/Simulations/f15/031/f15031b9680ce3490833380d4a94f40a270fb89f/75ff31fe588d7d0b2f330a693cba4f99c7ebef05/README.yaml +++ b/Simulations/f15/031/f15031b9680ce3490833380d4a94f40a270fb89f/75ff31fe588d7d0b2f330a693cba4f99c7ebef05/README.yaml @@ -55,9 +55,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 212 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPS/POT (83:8:8) bilayer at 298 K (ECC-lipids, SPC water model, ECC-ions, GROMACS 2018.0, 984 ns) [NMRlipids simulation 212] + name: Molecular dynamics trajectory of a POPC/POPS/POT (83:8:8) bilayer at 298 K + (ECC-lipids, SPC water model, ECC-ions, GROMACS 2018.0, 984 ns) [NMRlipids simulation + 212] alternateName: 6POPS_60POPC_3600SOL_6POT_298K_ECC-lipid - description: Molecular dynamics trajectory of a lipid bilayer of 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 83 mol%), 6 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 8 mol%) and 6 POT (8 mol%) at 298 K. Simulated with ECC-lipids, SPC water model, ECC-ions in GROMACS 2018.0 for 984 ns (19608 atoms). Deposited as NMRlipids Databank simulation 212 and available from https://doi.org/10.5281/zenodo.1488094. + description: Molecular dynamics trajectory of a lipid bilayer of 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 83 mol%), 6 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 8 mol%) + and 6 POT (8 mol%) at 298 K. Simulated with ECC-lipids, SPC water model, ECC-ions + in GROMACS 2018.0 for 984 ns (19608 atoms). Deposited as NMRlipids Databank simulation + 212 and available from https://doi.org/10.5281/zenodo.1488094. sameAs: https://doi.org/10.5281/zenodo.1488094 datePublished: '2018-11-14' license: @@ -148,7 +154,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1488094 identifier: 10.5281/zenodo.1488094 url: https://doi.org/10.5281/zenodo.1488094 - name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS (various mixtures) with ECC-lipids force field, and Na+ (K+) counterions + name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS + (various mixtures) with ECC-lipids force field, and Na+ (K+) counterions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/f18/90e/f1890ef3c2c8e86b83f8172de33b715aa3ff669a/29133fd9539e99260efc08ba5a65772c77d9ff90/README.yaml b/Simulations/f18/90e/f1890ef3c2c8e86b83f8172de33b715aa3ff669a/29133fd9539e99260efc08ba5a65772c77d9ff90/README.yaml index 06580c2f4f..74a73c87a9 100644 --- a/Simulations/f18/90e/f1890ef3c2c8e86b83f8172de33b715aa3ff669a/29133fd9539e99260efc08ba5a65772c77d9ff90/README.yaml +++ b/Simulations/f18/90e/f1890ef3c2c8e86b83f8172de33b715aa3ff669a/29133fd9539e99260efc08ba5a65772c77d9ff90/README.yaml @@ -50,9 +50,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 403 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (70:30) bilayer at 303.15 K (CHARMM36, GROMACS 5.1.2, 200 ns) [NMRlipids simulation 403] + name: Molecular dynamics trajectory of a POPC/CHOL (70:30) bilayer at 303.15 K (CHARMM36, + GROMACS 5.1.2, 200 ns) [NMRlipids simulation 403] alternateName: 84POPC_4800SOL_36CHOL_303K - description: Molecular dynamics trajectory of a lipid bilayer of 84 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 70 mol%) and 36 CHOL (cholesterol, 30 mol%) at 303.15 K. Simulated with CHARMM36 in GROMACS 5.1.2 for 200 ns (28320 atoms). Deposited as NMRlipids Databank simulation 403 and available from https://doi.org/10.5281/zenodo.163336. + description: Molecular dynamics trajectory of a lipid bilayer of 84 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 70 mol%) and 36 CHOL (cholesterol, 30 mol%) at 303.15 K. Simulated with CHARMM36 + in GROMACS 5.1.2 for 200 ns (28320 atoms). Deposited as NMRlipids Databank simulation + 403 and available from https://doi.org/10.5281/zenodo.163336. sameAs: https://doi.org/10.5281/zenodo.163336 datePublished: '2016-10-26' license: @@ -140,7 +144,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.163336 identifier: 10.5281/zenodo.163336 url: https://doi.org/10.5281/zenodo.163336 - name: Popc/Cholesterol (70:30) Lipid Membrane, 303K, Charmm36 Force Field, Simulation Files And 200 Ns Trajectory For Gromacs Md Simulation Engine V5.1.2 + name: Popc/Cholesterol (70:30) Lipid Membrane, 303K, Charmm36 Force Field, Simulation + Files And 200 Ns Trajectory For Gromacs Md Simulation Engine V5.1.2 publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/f1c/b0f/f1cb0f7b3e7f2d34b844bd3ec237bfa4fe845e87/3dc850ad50ed06ef9677f7c6520756fdf2962880/README.yaml b/Simulations/f1c/b0f/f1cb0f7b3e7f2d34b844bd3ec237bfa4fe845e87/3dc850ad50ed06ef9677f7c6520756fdf2962880/README.yaml index 8dfe1df222..6f3615d107 100644 --- a/Simulations/f1c/b0f/f1cb0f7b3e7f2d34b844bd3ec237bfa4fe845e87/3dc850ad50ed06ef9677f7c6520756fdf2962880/README.yaml +++ b/Simulations/f1c/b0f/f1cb0f7b3e7f2d34b844bd3ec237bfa4fe845e87/3dc850ad50ed06ef9677f7c6520756fdf2962880/README.yaml @@ -41,9 +41,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 378 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 298 K (MacRog, GROMACS 4.5.5, 50 ns) [NMRlipids simulation 378] + name: Molecular dynamics trajectory of a POPC bilayer at 298 K (MacRog, GROMACS + 4.5.5, 50 ns) [NMRlipids simulation 378] alternateName: 288POPC_1440SOL_298K - description: Molecular dynamics trajectory of a lipid bilayer of 288 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 298 K. Simulated with MacRog in GROMACS 4.5.5 for 50 ns (42912 atoms). Deposited as NMRlipids Databank simulation 378 and available from https://doi.org/10.5281/zenodo.13498. + description: Molecular dynamics trajectory of a lipid bilayer of 288 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 298 K. Simulated with MacRog in GROMACS 4.5.5 for 50 ns (42912 atoms). Deposited + as NMRlipids Databank simulation 378 and available from https://doi.org/10.5281/zenodo.13498. sameAs: https://doi.org/10.5281/zenodo.13498 datePublished: '2014-12-30' license: diff --git a/Simulations/f21/721/f21721495bce90381d9f105be56279fdc352b1be/c7d0765ac281c002f6387126b735109174ed6092/README.yaml b/Simulations/f21/721/f21721495bce90381d9f105be56279fdc352b1be/c7d0765ac281c002f6387126b735109174ed6092/README.yaml index 1e58d09d92..2edfdcb207 100644 --- a/Simulations/f21/721/f21721495bce90381d9f105be56279fdc352b1be/c7d0765ac281c002f6387126b735109174ed6092/README.yaml +++ b/Simulations/f21/721/f21721495bce90381d9f105be56279fdc352b1be/c7d0765ac281c002f6387126b735109174ed6092/README.yaml @@ -50,9 +50,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 36 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/CLA/SOD (82:9:9) bilayer at 315 K (CHARMM36, GROMACS 5.0.4, 500 ns) [NMRlipids simulation 36] + name: Molecular dynamics trajectory of a DPPC/CLA/SOD (82:9:9) bilayer at 315 K + (CHARMM36, GROMACS 5.0.4, 500 ns) [NMRlipids simulation 36] alternateName: DPPC_512_NaCl_150mM_315K_v-rescale - description: Molecular dynamics trajectory of a lipid bilayer of 512 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 82 mol%), 55 CLA (9 mol%) and 55 SOD (9 mol%) at 315 K. Simulated with CHARMM36 in GROMACS 5.0.4 for 500 ns (128110 atoms). Deposited as NMRlipids Databank simulation 36 and available from https://doi.org/10.5281/zenodo.1009027. + description: Molecular dynamics trajectory of a lipid bilayer of 512 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 82 mol%), 55 CLA (9 mol%) and 55 SOD (9 mol%) at 315 K. Simulated with CHARMM36 + in GROMACS 5.0.4 for 500 ns (128110 atoms). Deposited as NMRlipids Databank simulation + 36 and available from https://doi.org/10.5281/zenodo.1009027. sameAs: https://doi.org/10.5281/zenodo.1009027 datePublished: '2017-10-11' license: diff --git a/Simulations/f22/76d/f2276d44a27ada33b2326df41b2efb2c11eb8858/0b38528bf0ba9219523d4b17babddb3f28129873/README.yaml b/Simulations/f22/76d/f2276d44a27ada33b2326df41b2efb2c11eb8858/0b38528bf0ba9219523d4b17babddb3f28129873/README.yaml index 6b5ede4e1a..5e9445dc0a 100644 --- a/Simulations/f22/76d/f2276d44a27ada33b2326df41b2efb2c11eb8858/0b38528bf0ba9219523d4b17babddb3f28129873/README.yaml +++ b/Simulations/f22/76d/f2276d44a27ada33b2326df41b2efb2c11eb8858/0b38528bf0ba9219523d4b17babddb3f28129873/README.yaml @@ -50,9 +50,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/5 ID: 687 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (80:20) bilayer at 298.15 K (Slipids, GROMACS 2021, 1001 ns) [NMRlipids simulation 687] + name: Molecular dynamics trajectory of a POPC/CHOL (80:20) bilayer at 298.15 K (Slipids, + GROMACS 2021, 1001 ns) [NMRlipids simulation 687] alternateName: Slipids_POPC_CHOL20_M - description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 80 mol%) and 64 CHOL (cholesterol, 20 mol%) at 298.15 K. Simulated with Slipids in GROMACS 2021 for 1001 ns (87040 atoms). Deposited as NMRlipids Databank simulation 687 and available from https://doi.org/10.5281/zenodo.7022749. + description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 80 mol%) and 64 CHOL (cholesterol, 20 mol%) at 298.15 K. Simulated with Slipids + in GROMACS 2021 for 1001 ns (87040 atoms). Deposited as NMRlipids Databank simulation + 687 and available from https://doi.org/10.5281/zenodo.7022749. sameAs: https://doi.org/10.5281/zenodo.7022749 datePublished: '2022-08-23' license: diff --git a/Simulations/f28/def/f28defe4ba1cde035aca75a81dc1c2172af4a3be/1a8dbb3feecb935c132ae1d2dadcdb3f1ef33588/README.yaml b/Simulations/f28/def/f28defe4ba1cde035aca75a81dc1c2172af4a3be/1a8dbb3feecb935c132ae1d2dadcdb3f1ef33588/README.yaml index 470ca9dcd1..dc3dd3a9d5 100644 --- a/Simulations/f28/def/f28defe4ba1cde035aca75a81dc1c2172af4a3be/1a8dbb3feecb935c132ae1d2dadcdb3f1ef33588/README.yaml +++ b/Simulations/f28/def/f28defe4ba1cde035aca75a81dc1c2172af4a3be/1a8dbb3feecb935c132ae1d2dadcdb3f1ef33588/README.yaml @@ -53,9 +53,14 @@ EXPERIMENT: TOCL: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a SOD/TOCL/CLA (65:30:5) bilayer at 303.15 K (Charmm36, GROMACS 2023.2, 500 ns) [NMRlipids simulation 824] + name: Molecular dynamics trajectory of a SOD/TOCL/CLA (65:30:5) bilayer at 303.15 + K (Charmm36, GROMACS 2023.2, 500 ns) [NMRlipids simulation 824] alternateName: TOCL_66_Na_Cl_T303_40w/P - description: Molecular dynamics trajectory of a lipid bilayer of 143 SOD (65 mol%), 66 TOCL (1’,3’-Bis[1,2-dioleoyl-sn-glycero-3-phospho]-glycerol, 30 mol%) and 11 CLA (5 mol%) at 303.15 K. Simulated with Charmm36 in GROMACS 2023.2 for 500 ns (32362 atoms). Deposited as NMRlipids Databank simulation 824 and available from https://doi.org/10.5281/zenodo.13933145. + description: Molecular dynamics trajectory of a lipid bilayer of 143 SOD (65 mol%), + 66 TOCL (1’,3’-Bis[1,2-dioleoyl-sn-glycero-3-phospho]-glycerol, 30 mol%) and 11 + CLA (5 mol%) at 303.15 K. Simulated with Charmm36 in GROMACS 2023.2 for 500 ns + (32362 atoms). Deposited as NMRlipids Databank simulation 824 and available from + https://doi.org/10.5281/zenodo.13933145. sameAs: https://doi.org/10.5281/zenodo.13933145 datePublished: '2024-10-15' license: diff --git a/Simulations/f2e/6ef/f2e6efcbecac5edb155ab3c7264a44b2b0255abf/3f397dc2f9212a0bdd1e40ab9d6b5d44488d9725/README.yaml b/Simulations/f2e/6ef/f2e6efcbecac5edb155ab3c7264a44b2b0255abf/3f397dc2f9212a0bdd1e40ab9d6b5d44488d9725/README.yaml index 1ac06dfee2..053a7e7f4a 100644 --- a/Simulations/f2e/6ef/f2e6efcbecac5edb155ab3c7264a44b2b0255abf/3f397dc2f9212a0bdd1e40ab9d6b5d44488d9725/README.yaml +++ b/Simulations/f2e/6ef/f2e6efcbecac5edb155ab3c7264a44b2b0255abf/3f397dc2f9212a0bdd1e40ab9d6b5d44488d9725/README.yaml @@ -44,9 +44,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 619 bioschema_properties: - name: Molecular dynamics trajectory of a DOPE bilayer at 271 K (GROMOS-CKP, GROMACS 5.0.6, 400 ns) [NMRlipids simulation 619] + name: Molecular dynamics trajectory of a DOPE bilayer at 271 K (GROMOS-CKP, GROMACS + 5.0.6, 400 ns) [NMRlipids simulation 619] alternateName: 128DOPE_4789SOL_271K_GROMOS-CKP_v1 - description: Molecular dynamics trajectory of a lipid bilayer of 128 DOPE (1,2-dioleoyl-sn-glycero-3-phosphoethanolamine) at 271 K. Simulated with GROMOS-CKP in GROMACS 5.0.6 for 400 ns (21279 atoms). Deposited as NMRlipids Databank simulation 619 and available from https://doi.org/10.5281/zenodo.1293941. + description: Molecular dynamics trajectory of a lipid bilayer of 128 DOPE (1,2-dioleoyl-sn-glycero-3-phosphoethanolamine) + at 271 K. Simulated with GROMOS-CKP in GROMACS 5.0.6 for 400 ns (21279 atoms). + Deposited as NMRlipids Databank simulation 619 and available from https://doi.org/10.5281/zenodo.1293941. sameAs: https://doi.org/10.5281/zenodo.1293941 datePublished: '2018-06-20' license: diff --git a/Simulations/f31/0bd/f310bd1589844f2402c3096357d1ba41b57d8829/07ade0eade753c9826df16a5e5707e5db67f44d8/README.yaml b/Simulations/f31/0bd/f310bd1589844f2402c3096357d1ba41b57d8829/07ade0eade753c9826df16a5e5707e5db67f44d8/README.yaml index ada7c09c13..879d32dc6a 100644 --- a/Simulations/f31/0bd/f310bd1589844f2402c3096357d1ba41b57d8829/07ade0eade753c9826df16a5e5707e5db67f44d8/README.yaml +++ b/Simulations/f31/0bd/f310bd1589844f2402c3096357d1ba41b57d8829/07ade0eade753c9826df16a5e5707e5db67f44d8/README.yaml @@ -45,9 +45,12 @@ EXPERIMENT: - 10.1016/j.bbamem.2011.07.022/2 ID: 90 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 303 K (CHARMM36 noNBFIX, GROMACS, 298 ns) [NMRlipids simulation 90] + name: Molecular dynamics trajectory of a POPC bilayer at 303 K (CHARMM36 noNBFIX, + GROMACS, 298 ns) [NMRlipids simulation 90] alternateName: 200POPC_9000SOL_303K_noNBFIX - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 303 K. Simulated with CHARMM36 noNBFIX in GROMACS for 298 ns (53800 atoms). Deposited as NMRlipids Databank simulation 90 and available from https://doi.org/10.5281/zenodo.3434396. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 303 K. Simulated with CHARMM36 noNBFIX in GROMACS for 298 ns (53800 atoms). + Deposited as NMRlipids Databank simulation 90 and available from https://doi.org/10.5281/zenodo.3434396. sameAs: https://doi.org/10.5281/zenodo.3434396 datePublished: '2019-09-17' license: diff --git a/Simulations/f32/81d/f3281d1071b0644075df0156d7233bd1109e99dd/8788d2e0768fe7e7e9784d3990494716071c627c/README.yaml b/Simulations/f32/81d/f3281d1071b0644075df0156d7233bd1109e99dd/8788d2e0768fe7e7e9784d3990494716071c627c/README.yaml index ff28cf3a3d..65e0c58a6f 100644 --- a/Simulations/f32/81d/f3281d1071b0644075df0156d7233bd1109e99dd/8788d2e0768fe7e7e9784d3990494716071c627c/README.yaml +++ b/Simulations/f32/81d/f3281d1071b0644075df0156d7233bd1109e99dd/8788d2e0768fe7e7e9784d3990494716071c627c/README.yaml @@ -51,9 +51,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/8 ID: 688 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (62:38) bilayer at 298.15 K (Lipid17, GROMACS 2021, 1001 ns) [NMRlipids simulation 688] + name: Molecular dynamics trajectory of a POPC/CHOL (62:38) bilayer at 298.15 K (Lipid17, + GROMACS 2021, 1001 ns) [NMRlipids simulation 688] alternateName: Lipid17_POPC_CHOL38_S - description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 62 mol%) and 40 CHOL (cholesterol, 38 mol%) at 298.15 K. Simulated with Lipid17 in GROMACS 2021 for 1001 ns (27136 atoms). Deposited as NMRlipids Databank simulation 688 and available from https://doi.org/10.5281/zenodo.6992065. + description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 62 mol%) and 40 CHOL (cholesterol, 38 mol%) at 298.15 K. Simulated with Lipid17 + in GROMACS 2021 for 1001 ns (27136 atoms). Deposited as NMRlipids Databank simulation + 688 and available from https://doi.org/10.5281/zenodo.6992065. sameAs: https://doi.org/10.5281/zenodo.6992065 datePublished: '2022-08-15' license: diff --git a/Simulations/f40/bb6/f40bb6ab5d44402be07059e8df74b5a8200f031e/6774168dfec0a5a7377c8a46341eba603f320cf7/README.yaml b/Simulations/f40/bb6/f40bb6ab5d44402be07059e8df74b5a8200f031e/6774168dfec0a5a7377c8a46341eba603f320cf7/README.yaml index 03ac16abed..4c94b2e1dc 100644 --- a/Simulations/f40/bb6/f40bb6ab5d44402be07059e8df74b5a8200f031e/6774168dfec0a5a7377c8a46341eba603f320cf7/README.yaml +++ b/Simulations/f40/bb6/f40bb6ab5d44402be07059e8df74b5a8200f031e/6774168dfec0a5a7377c8a46341eba603f320cf7/README.yaml @@ -45,9 +45,13 @@ DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 106 AUTHORS_CONTACT: Thomas Piggot bioschema_properties: - name: Molecular dynamics trajectory of a POPS/SOD (50:50) bilayer at 298 K (CHARMM36, GROMACS, 100 ns) [NMRlipids simulation 106] + name: Molecular dynamics trajectory of a POPS/SOD (50:50) bilayer at 298 K (CHARMM36, + GROMACS, 100 ns) [NMRlipids simulation 106] alternateName: POPS_298K - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 50 mol%) and 128 SOD (50 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for 100 ns (29824 atoms). Deposited as NMRlipids Databank simulation 106 and available from https://doi.org/10.5281/zenodo.1129415. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, + 50 mol%) and 128 SOD (50 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for + 100 ns (29824 atoms). Deposited as NMRlipids Databank simulation 106 and available + from https://doi.org/10.5281/zenodo.1129415. sameAs: https://doi.org/10.5281/zenodo.1129415 datePublished: '2017-12-24' license: diff --git a/Simulations/f4e/86b/f4e86b908e89c8cb17a42762c4a145f9d9aeb84d/2ef5622f8b68ac698206dd818d27e4b12e2d2afd/README.yaml b/Simulations/f4e/86b/f4e86b908e89c8cb17a42762c4a145f9d9aeb84d/2ef5622f8b68ac698206dd818d27e4b12e2d2afd/README.yaml index 79e531e0a1..688edcd9d6 100644 --- a/Simulations/f4e/86b/f4e86b908e89c8cb17a42762c4a145f9d9aeb84d/2ef5622f8b68ac698206dd818d27e4b12e2d2afd/README.yaml +++ b/Simulations/f4e/86b/f4e86b908e89c8cb17a42762c4a145f9d9aeb84d/2ef5622f8b68ac698206dd818d27e4b12e2d2afd/README.yaml @@ -50,9 +50,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/3 ID: 689 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (89:11) bilayer at 298.15 K (Lipid17, GROMACS 2021, 1001 ns) [NMRlipids simulation 689] + name: Molecular dynamics trajectory of a POPC/CHOL (89:11) bilayer at 298.15 K (Lipid17, + GROMACS 2021, 1001 ns) [NMRlipids simulation 689] alternateName: Lipid17_POPC_CHOL11_M - description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 89 mol%) and 32 CHOL (cholesterol, 11 mol%) at 298.15 K. Simulated with Lipid17 in GROMACS 2021 for 1001 ns (79872 atoms). Deposited as NMRlipids Databank simulation 689 and available from https://doi.org/10.5281/zenodo.6992065. + description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 89 mol%) and 32 CHOL (cholesterol, 11 mol%) at 298.15 K. Simulated with Lipid17 + in GROMACS 2021 for 1001 ns (79872 atoms). Deposited as NMRlipids Databank simulation + 689 and available from https://doi.org/10.5281/zenodo.6992065. sameAs: https://doi.org/10.5281/zenodo.6992065 datePublished: '2022-08-15' license: diff --git a/Simulations/f56/a8b/f56a8b60e2500b0bf1c438187d8767fe79000b1e/232dca8fef7c81b3e0438d0ebdc2997f17df898e/README.yaml b/Simulations/f56/a8b/f56a8b60e2500b0bf1c438187d8767fe79000b1e/232dca8fef7c81b3e0438d0ebdc2997f17df898e/README.yaml index e3a0e23deb..32e4682de6 100644 --- a/Simulations/f56/a8b/f56a8b60e2500b0bf1c438187d8767fe79000b1e/232dca8fef7c81b3e0438d0ebdc2997f17df898e/README.yaml +++ b/Simulations/f56/a8b/f56a8b60e2500b0bf1c438187d8767fe79000b1e/232dca8fef7c81b3e0438d0ebdc2997f17df898e/README.yaml @@ -57,9 +57,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 461 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/DHMDMAB (54:23:23) bilayer at 313 K (ECC-lipids, GROMACS 5.1.4, 200 ns) [NMRlipids simulation 461] + name: Molecular dynamics trajectory of a POPC/CLA/DHMDMAB (54:23:23) bilayer at + 313 K (ECC-lipids, GROMACS 5.1.4, 200 ns) [NMRlipids simulation 461] alternateName: 100POPC_6214SOL_42DHMDMAB_42CLA_313K_SPCEmodel - description: Molecular dynamics trajectory of a lipid bilayer of 100 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 54 mol%), 42 CLA (23 mol%) and 42 DHMDMAB (dihexadecyldimethylammonium, 23 mol%) at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 200 ns (36578 atoms). Deposited as NMRlipids Databank simulation 461 and available from https://doi.org/10.5281/zenodo.1118682. + description: Molecular dynamics trajectory of a lipid bilayer of 100 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 54 mol%), 42 CLA (23 mol%) and 42 DHMDMAB (dihexadecyldimethylammonium, 23 mol%) + at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 200 ns (36578 atoms). + Deposited as NMRlipids Databank simulation 461 and available from https://doi.org/10.5281/zenodo.1118682. sameAs: https://doi.org/10.5281/zenodo.1118682 datePublished: '2017-12-19' license: @@ -150,7 +154,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1118682 identifier: 10.5281/zenodo.1118682 url: https://doi.org/10.5281/zenodo.1118682 - name: Simulations Of Popc Lipid Bilayer In Water Solution With Various Molar Fractions Of Cationic Surfactant Dihexadecylammonium Using Ecc-Popc Force Field + name: Simulations Of Popc Lipid Bilayer In Water Solution With Various Molar Fractions + Of Cationic Surfactant Dihexadecylammonium Using Ecc-Popc Force Field publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/f58/356/f583561f9fdda76cba873d4a49d39f59818a0767/bde7de03e1e058c7b591ba99895bb94bfbe8a636/README.yaml b/Simulations/f58/356/f583561f9fdda76cba873d4a49d39f59818a0767/bde7de03e1e058c7b591ba99895bb94bfbe8a636/README.yaml index c026cc3ac5..cd2b124488 100644 --- a/Simulations/f58/356/f583561f9fdda76cba873d4a49d39f59818a0767/bde7de03e1e058c7b591ba99895bb94bfbe8a636/README.yaml +++ b/Simulations/f58/356/f583561f9fdda76cba873d4a49d39f59818a0767/bde7de03e1e058c7b591ba99895bb94bfbe8a636/README.yaml @@ -42,9 +42,12 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 591 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 303 K (Slipids2020, GROMACS GROMACS 2019, 268 ns) [NMRlipids simulation 591] + name: Molecular dynamics trajectory of a POPC bilayer at 303 K (Slipids2020, GROMACS + GROMACS 2019, 268 ns) [NMRlipids simulation 591] alternateName: POPC bilayer 303 K - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 303 K. Simulated with Slipids2020 in GROMACS GROMACS 2019 for 268 ns (32512 atoms). Deposited as NMRlipids Databank simulation 591 and available from https://doi.org/10.5281/zenodo.4683633. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 303 K. Simulated with Slipids2020 in GROMACS GROMACS 2019 for 268 ns (32512 + atoms). Deposited as NMRlipids Databank simulation 591 and available from https://doi.org/10.5281/zenodo.4683633. sameAs: https://doi.org/10.5281/zenodo.4683633 datePublished: '2020-09-14' license: @@ -134,7 +137,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.4683633 identifier: 10.5281/zenodo.4683633 url: https://doi.org/10.5281/zenodo.4683633 - name: Optimization of Slipids Force Field Parameters Describing Headgroups of Phospholipids + name: Optimization of Slipids Force Field Parameters Describing Headgroups of + Phospholipids publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/f5d/6d3/f5d6d3f7e54bde318254a0476d92b40cf73b92a2/5c2318b611ae263ecdd773eb635f193b38737105/README.yaml b/Simulations/f5d/6d3/f5d6d3f7e54bde318254a0476d92b40cf73b92a2/5c2318b611ae263ecdd773eb635f193b38737105/README.yaml index eadd51190e..adb29321bb 100644 --- a/Simulations/f5d/6d3/f5d6d3f7e54bde318254a0476d92b40cf73b92a2/5c2318b611ae263ecdd773eb635f193b38737105/README.yaml +++ b/Simulations/f5d/6d3/f5d6d3f7e54bde318254a0476d92b40cf73b92a2/5c2318b611ae263ecdd773eb635f193b38737105/README.yaml @@ -50,9 +50,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 46 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/CLA/SOD (83:9:9) bilayer at 293 K (Slipids for lipids and Smith & Dang for ions, GROMACS 4.6, 200 ns) [NMRlipids simulation 46] + name: Molecular dynamics trajectory of a DPPC/CLA/SOD (83:9:9) bilayer at 293 K + (Slipids for lipids and Smith & Dang for ions, GROMACS 4.6, 200 ns) [NMRlipids + simulation 46] alternateName: 200DOPC_9000SOL_21SOD_21CLA_293K - description: Molecular dynamics trajectory of a lipid bilayer of 200 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 83 mol%), 21 CLA (9 mol%) and 21 SOD (9 mol%) at 293 K. Simulated with Slipids for lipids and Smith & Dang for ions in GROMACS 4.6 for 200 ns (53042 atoms). Deposited as NMRlipids Databank simulation 46 and available from https://doi.org/10.5281/zenodo.259443. + description: Molecular dynamics trajectory of a lipid bilayer of 200 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 83 mol%), 21 CLA (9 mol%) and 21 SOD (9 mol%) at 293 K. Simulated with Slipids + for lipids and Smith & Dang for ions in GROMACS 4.6 for 200 ns (53042 atoms). + Deposited as NMRlipids Databank simulation 46 and available from https://doi.org/10.5281/zenodo.259443. sameAs: https://doi.org/10.5281/zenodo.259443 datePublished: '2017-01-24' license: diff --git a/Simulations/f62/739/f627391cd6cddf82078a7a12c4cd22767535b6fe/d9c93bb0ae93ede37c230593a348691012519efc/README.yaml b/Simulations/f62/739/f627391cd6cddf82078a7a12c4cd22767535b6fe/d9c93bb0ae93ede37c230593a348691012519efc/README.yaml index 2139b23394..20bdeee8f5 100644 --- a/Simulations/f62/739/f627391cd6cddf82078a7a12c4cd22767535b6fe/d9c93bb0ae93ede37c230593a348691012519efc/README.yaml +++ b/Simulations/f62/739/f627391cd6cddf82078a7a12c4cd22767535b6fe/d9c93bb0ae93ede37c230593a348691012519efc/README.yaml @@ -55,9 +55,15 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/10 ID: 299 bioschema_properties: - name: Molecular dynamics trajectory of a CHOL/POPC (50:50) bilayer at 298 K (Berger and Modified Höltje model for cholesterol, GROMACS 4.5, 50 ns) [NMRlipids simulation 299] + name: Molecular dynamics trajectory of a CHOL/POPC (50:50) bilayer at 298 K (Berger + and Modified Höltje model for cholesterol, GROMACS 4.5, 50 ns) [NMRlipids simulation + 299] alternateName: 64CHOL_64POPC_10314SOL_298K_Berger - description: Molecular dynamics trajectory of a lipid bilayer of 64 CHOL (cholesterol, 50 mol%) and 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 50 mol%) at 298 K. Simulated with Berger and Modified Höltje model for cholesterol in GROMACS 4.5 for 50 ns (36126 atoms). Deposited as NMRlipids Databank simulation 299 and available from https://doi.org/10.5281/zenodo.4643862. + description: Molecular dynamics trajectory of a lipid bilayer of 64 CHOL (cholesterol, + 50 mol%) and 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 50 mol%) + at 298 K. Simulated with Berger and Modified Höltje model for cholesterol in GROMACS + 4.5 for 50 ns (36126 atoms). Deposited as NMRlipids Databank simulation 299 and + available from https://doi.org/10.5281/zenodo.4643862. sameAs: https://doi.org/10.5281/zenodo.4643862 datePublished: '2014-12-17' license: @@ -153,7 +159,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.4643862 identifier: 10.5281/zenodo.4643862 url: https://doi.org/10.5281/zenodo.4643862 - name: MD simulation trajectory and related files for POPC/cholesterol (50 mol%) bilayer (Berger model delivered by Tieleman, modified Höltje, Gromacs 4.5) + name: MD simulation trajectory and related files for POPC/cholesterol (50 mol%) + bilayer (Berger model delivered by Tieleman, modified Höltje, Gromacs 4.5) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/f71/3e1/f713e1a9cd7106214201b4b39400c4701db17688/0be798e43b10a090bdccd67fddfa4c68cd094188/README.yaml b/Simulations/f71/3e1/f713e1a9cd7106214201b4b39400c4701db17688/0be798e43b10a090bdccd67fddfa4c68cd094188/README.yaml index 4ee41f05e0..c44ba804e0 100644 --- a/Simulations/f71/3e1/f713e1a9cd7106214201b4b39400c4701db17688/0be798e43b10a090bdccd67fddfa4c68cd094188/README.yaml +++ b/Simulations/f71/3e1/f713e1a9cd7106214201b4b39400c4701db17688/0be798e43b10a090bdccd67fddfa4c68cd094188/README.yaml @@ -67,9 +67,15 @@ EXPERIMENT: SAPI25: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POT/CHOL/CLA/SAPI25 (46:22:21:7:4) bilayer at 298.15 K (CHARMM36m, GROMACS 2020.1, 1202 ns) [NMRlipids simulation 781] + name: Molecular dynamics trajectory of a POPC/POT/CHOL/CLA/SAPI25 (46:22:21:7:4) + bilayer at 298.15 K (CHARMM36m, GROMACS 2020.1, 1202 ns) [NMRlipids simulation + 781] alternateName: POPC_194_SAPI25_16_CHOL_90_KCl_150mM_298.15K - description: Molecular dynamics trajectory of a lipid bilayer of 194 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 46 mol%), 94 POT (22 mol%), 90 CHOL (cholesterol, 21 mol%), 30 CLA (7 mol%) and 16 SAPI25 (1-stearoyl-2-arachidonoyl-sn-phosphatidylinositol 4,5-biphosphate, 4 mol%) at 298.15 K. Simulated with CHARMM36m in GROMACS 2020.1 for 1202 ns (70268 atoms). Deposited as NMRlipids Databank simulation 781 and available from https://doi.org/10.5281/zenodo.8370442. + description: Molecular dynamics trajectory of a lipid bilayer of 194 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 46 mol%), 94 POT (22 mol%), 90 CHOL (cholesterol, 21 mol%), 30 CLA (7 mol%) and + 16 SAPI25 (1-stearoyl-2-arachidonoyl-sn-phosphatidylinositol 4,5-biphosphate, + 4 mol%) at 298.15 K. Simulated with CHARMM36m in GROMACS 2020.1 for 1202 ns (70268 + atoms). Deposited as NMRlipids Databank simulation 781 and available from https://doi.org/10.5281/zenodo.8370442. sameAs: https://doi.org/10.5281/zenodo.8370442 datePublished: '2023-09-22' license: diff --git a/Simulations/f71/e45/f71e45bd3af12a8f3b9b7fbefb075cd07a3c5afa/0b2f43dc827fd9f81998e182746684ed74a73124/README.yaml b/Simulations/f71/e45/f71e45bd3af12a8f3b9b7fbefb075cd07a3c5afa/0b2f43dc827fd9f81998e182746684ed74a73124/README.yaml index 3c6878a656..7f8e86dc69 100644 --- a/Simulations/f71/e45/f71e45bd3af12a8f3b9b7fbefb075cd07a3c5afa/0b2f43dc827fd9f81998e182746684ed74a73124/README.yaml +++ b/Simulations/f71/e45/f71e45bd3af12a8f3b9b7fbefb075cd07a3c5afa/0b2f43dc827fd9f81998e182746684ed74a73124/README.yaml @@ -59,9 +59,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 200 bioschema_properties: - name: Molecular dynamics trajectory of a SOD/CLA/POPC/POPS (39:34:22:4) bilayer at 298 K (Lipid17 and Dang ions, GROMACS 2018.0, 1000 ns) [NMRlipids simulation 200] + name: Molecular dynamics trajectory of a SOD/CLA/POPC/POPS (39:34:22:4) bilayer + at 298 K (Lipid17 and Dang ions, GROMACS 2018.0, 1000 ns) [NMRlipids simulation + 200] alternateName: 12POPS_60POPC_3377SOL_104SOD_92CLA_298K - description: Molecular dynamics trajectory of a lipid bilayer of 104 SOD (39 mol%), 92 CLA (34 mol%), 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 22 mol%) and 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 4 mol%) at 298 K. Simulated with Lipid17 and Dang ions in GROMACS 2018.0 for 1000 ns (19891 atoms). Deposited as NMRlipids Databank simulation 200 and available from https://doi.org/10.5281/zenodo.1487895. + description: Molecular dynamics trajectory of a lipid bilayer of 104 SOD (39 mol%), + 92 CLA (34 mol%), 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 22 + mol%) and 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 4 mol%) + at 298 K. Simulated with Lipid17 and Dang ions in GROMACS 2018.0 for 1000 ns (19891 + atoms). Deposited as NMRlipids Databank simulation 200 and available from https://doi.org/10.5281/zenodo.1487895. sameAs: https://doi.org/10.5281/zenodo.1487895 datePublished: '2018-11-14' license: @@ -153,7 +159,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1487895 identifier: 10.5281/zenodo.1487895 url: https://doi.org/10.5281/zenodo.1487895 - name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS with the lipid17 force field, NaCl and KCl salt concentrations + name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS + with the lipid17 force field, NaCl and KCl salt concentrations publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/f74/535/f74535fd6e9a5a2924b439c507fcb58b649628ef/44fcc2df562e7de6459f296386497be981b3b7e5/README.yaml b/Simulations/f74/535/f74535fd6e9a5a2924b439c507fcb58b649628ef/44fcc2df562e7de6459f296386497be981b3b7e5/README.yaml index e4ff235eb1..470c172ea4 100644 --- a/Simulations/f74/535/f74535fd6e9a5a2924b439c507fcb58b649628ef/44fcc2df562e7de6459f296386497be981b3b7e5/README.yaml +++ b/Simulations/f74/535/f74535fd6e9a5a2924b439c507fcb58b649628ef/44fcc2df562e7de6459f296386497be981b3b7e5/README.yaml @@ -45,9 +45,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 379 bioschema_properties: - name: Molecular dynamics trajectory of a DLPC bilayer at 300 K (Berger-DLPC-13, GROMACS 4.5.4, 80 ns) [NMRlipids simulation 379] + name: Molecular dynamics trajectory of a DLPC bilayer at 300 K (Berger-DLPC-13, + GROMACS 4.5.4, 80 ns) [NMRlipids simulation 379] alternateName: 72DLPC_1728SOL_300K - description: Molecular dynamics trajectory of a lipid bilayer of 72 DLPC (1,2-dilauroyl-sn-glycero-3-phosphocholine) at 300 K. Simulated with Berger-DLPC-13 in GROMACS 4.5.4 for 80 ns (8208 atoms). Deposited as NMRlipids Databank simulation 379 and available from https://doi.org/10.5281/zenodo.16289. + description: Molecular dynamics trajectory of a lipid bilayer of 72 DLPC (1,2-dilauroyl-sn-glycero-3-phosphocholine) + at 300 K. Simulated with Berger-DLPC-13 in GROMACS 4.5.4 for 80 ns (8208 atoms). + Deposited as NMRlipids Databank simulation 379 and available from https://doi.org/10.5281/zenodo.16289. sameAs: https://doi.org/10.5281/zenodo.16289 datePublished: '2015-03-24' license: diff --git a/Simulations/f77/7b0/f777b003f2709874e8b5d1105371134abd08883c/e18894597f0961f3c72aa516f25104507dd30df5/README.yaml b/Simulations/f77/7b0/f777b003f2709874e8b5d1105371134abd08883c/e18894597f0961f3c72aa516f25104507dd30df5/README.yaml index 1be54c83e3..16fd25ec5b 100644 --- a/Simulations/f77/7b0/f777b003f2709874e8b5d1105371134abd08883c/e18894597f0961f3c72aa516f25104507dd30df5/README.yaml +++ b/Simulations/f77/7b0/f777b003f2709874e8b5d1105371134abd08883c/e18894597f0961f3c72aa516f25104507dd30df5/README.yaml @@ -49,9 +49,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 690 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (71:29) bilayer at 298.15 K (MacRog, GROMACS 2021, 1001 ns) [NMRlipids simulation 690] + name: Molecular dynamics trajectory of a POPC/CHOL (71:29) bilayer at 298.15 K (MacRog, + GROMACS 2021, 1001 ns) [NMRlipids simulation 690] alternateName: MacRog_POPC_CHOL29_S - description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 71 mol%) and 26 CHOL (cholesterol, 29 mol%) at 298.15 K. Simulated with MacRog in GROMACS 2021 for 1001 ns (24000 atoms). Deposited as NMRlipids Databank simulation 690 and available from https://doi.org/10.5281/zenodo.7061800. + description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 71 mol%) and 26 CHOL (cholesterol, 29 mol%) at 298.15 K. Simulated with MacRog + in GROMACS 2021 for 1001 ns (24000 atoms). Deposited as NMRlipids Databank simulation + 690 and available from https://doi.org/10.5281/zenodo.7061800. sameAs: https://doi.org/10.5281/zenodo.7061800 datePublished: '2022-09-08' license: diff --git a/Simulations/f77/7b3/f777b331c6644fa590a844c27121e5faca644413/97b177a99817aaa63cad63d3f51a70722a3f74d6/README.yaml b/Simulations/f77/7b3/f777b331c6644fa590a844c27121e5faca644413/97b177a99817aaa63cad63d3f51a70722a3f74d6/README.yaml index ca7aa7aad1..1b493bae66 100644 --- a/Simulations/f77/7b3/f777b331c6644fa590a844c27121e5faca644413/97b177a99817aaa63cad63d3f51a70722a3f74d6/README.yaml +++ b/Simulations/f77/7b3/f777b331c6644fa590a844c27121e5faca644413/97b177a99817aaa63cad63d3f51a70722a3f74d6/README.yaml @@ -50,9 +50,14 @@ EXPERIMENT: FORMFACTOR: [] ID: 392 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (48:35:17) bilayer at 310 K (Slipids with ECC-scaled ions (Kohagen), GROMACS 4.6, 600 ns) [NMRlipids simulation 392] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (48:35:17) bilayer at 310 + K (Slipids with ECC-scaled ions (Kohagen), GROMACS 4.6, 600 ns) [NMRlipids simulation + 392] alternateName: 200POPC_9000SOL_73CAL_146CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 48 mol%), 146 CLA (35 mol%) and 73 CAL (17 mol%) at 310 K. Simulated with Slipids with ECC-scaled ions (Kohagen) in GROMACS 4.6 for 600 ns (54019 atoms). Deposited as NMRlipids Databank simulation 392 and available from https://doi.org/10.5281/zenodo.259354. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 48 mol%), 146 CLA (35 mol%) and 73 CAL (17 mol%) at 310 K. Simulated with Slipids + with ECC-scaled ions (Kohagen) in GROMACS 4.6 for 600 ns (54019 atoms). Deposited + as NMRlipids Databank simulation 392 and available from https://doi.org/10.5281/zenodo.259354. sameAs: https://doi.org/10.5281/zenodo.259354 datePublished: '2017-01-24' license: @@ -140,7 +145,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.259354 identifier: 10.5281/zenodo.259354 url: https://doi.org/10.5281/zenodo.259354 - name: Popc With Varying Amounts Of Cholesterol, 450 Mm Of Cacl_2. Slipids With Ecc-Scaled Ions + name: Popc With Varying Amounts Of Cholesterol, 450 Mm Of Cacl_2. Slipids With + Ecc-Scaled Ions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/f78/e18/f78e188379aa6f6b1be9f2a8afc8bc2aac191ed0/443765a3de567fd6fe4e8666d29c63e8580e6306/README.yaml b/Simulations/f78/e18/f78e188379aa6f6b1be9f2a8afc8bc2aac191ed0/443765a3de567fd6fe4e8666d29c63e8580e6306/README.yaml index e6a8b56b0e..3eb48f4b7c 100644 --- a/Simulations/f78/e18/f78e188379aa6f6b1be9f2a8afc8bc2aac191ed0/443765a3de567fd6fe4e8666d29c63e8580e6306/README.yaml +++ b/Simulations/f78/e18/f78e188379aa6f6b1be9f2a8afc8bc2aac191ed0/443765a3de567fd6fe4e8666d29c63e8580e6306/README.yaml @@ -64,9 +64,16 @@ EXPERIMENT: FORMFACTOR: [] ID: 240 bioschema_properties: - name: Molecular dynamics trajectory of a CLA/DMTAP/SOD/DMPC (46:23:23:8) bilayer at 323 K (Berger with DMTAP modification by Gurtovenko et al., GROMACS 3.x, 110 ns) [NMRlipids simulation 240] + name: Molecular dynamics trajectory of a CLA/DMTAP/SOD/DMPC (46:23:23:8) bilayer + at 323 K (Berger with DMTAP modification by Gurtovenko et al., GROMACS 3.x, 110 + ns) [NMRlipids simulation 240] alternateName: 32DMPC_96DMTAP_96SOD_192CLA_5304SOL_323K - description: Molecular dynamics trajectory of a lipid bilayer of 192 CLA (46 mol%), 96 DMTAP (1,2-dimyristoyl-3-trimethylammonium-propane, 23 mol%), 96 SOD (23 mol%) and 32 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine, 8 mol%) at 323 K. Simulated with Berger with DMTAP modification by Gurtovenko et al. in GROMACS 3.x for 110 ns (21416 atoms). Deposited as NMRlipids Databank simulation 240 and available from https://doi.org/10.5281/zenodo.51750. + description: Molecular dynamics trajectory of a lipid bilayer of 192 CLA (46 mol%), + 96 DMTAP (1,2-dimyristoyl-3-trimethylammonium-propane, 23 mol%), 96 SOD (23 mol%) + and 32 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine, 8 mol%) at 323 K. Simulated + with Berger with DMTAP modification by Gurtovenko et al. in GROMACS 3.x for 110 + ns (21416 atoms). Deposited as NMRlipids Databank simulation 240 and available + from https://doi.org/10.5281/zenodo.51750. sameAs: https://doi.org/10.5281/zenodo.51750 datePublished: '2016-05-20' license: @@ -165,7 +172,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.51750 identifier: 10.5281/zenodo.51750 url: https://doi.org/10.5281/zenodo.51750 - name: 'Molecular dynamics simulation trajectory of a cationic lipid bilayer: 75/25 mol% DMTAP/DMPC in 1.0 M NaCl' + name: 'Molecular dynamics simulation trajectory of a cationic lipid bilayer: 75/25 + mol% DMTAP/DMPC in 1.0 M NaCl' publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/f7d/d0c/f7dd0ccee0149dc3104b9b31f6f8966d45c2d520/8b79c7ddba192facb419ac449b28d32804d9f882/README.yaml b/Simulations/f7d/d0c/f7dd0ccee0149dc3104b9b31f6f8966d45c2d520/8b79c7ddba192facb419ac449b28d32804d9f882/README.yaml index 02ba614b7a..dc442e2af3 100644 --- a/Simulations/f7d/d0c/f7dd0ccee0149dc3104b9b31f6f8966d45c2d520/8b79c7ddba192facb419ac449b28d32804d9f882/README.yaml +++ b/Simulations/f7d/d0c/f7dd0ccee0149dc3104b9b31f6f8966d45c2d520/8b79c7ddba192facb419ac449b28d32804d9f882/README.yaml @@ -44,9 +44,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 86 bioschema_properties: - name: Molecular dynamics trajectory of a POPE bilayer at 313 K (GROMOS 43A1-S3, GROMACS 4.0.7, 100 ns) [NMRlipids simulation 86] + name: Molecular dynamics trajectory of a POPE bilayer at 313 K (GROMOS 43A1-S3, + GROMACS 4.0.7, 100 ns) [NMRlipids simulation 86] alternateName: 128POPE_3552SOL_313K_v1 - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) at 313 K. Simulated with GROMOS 43A1-S3 in GROMACS 4.0.7 for 100 ns (17312 atoms). Deposited as NMRlipids Databank simulation 86 and available from https://doi.org/10.5281/zenodo.1293762. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) + at 313 K. Simulated with GROMOS 43A1-S3 in GROMACS 4.0.7 for 100 ns (17312 atoms). + Deposited as NMRlipids Databank simulation 86 and available from https://doi.org/10.5281/zenodo.1293762. sameAs: https://doi.org/10.5281/zenodo.1293762 datePublished: '2018-06-20' license: @@ -132,7 +135,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1293762 identifier: 10.5281/zenodo.1293762 url: https://doi.org/10.5281/zenodo.1293762 - name: 'Gromos 43A1-S3 Pope Simulations (Versions 1 And 2) 313 K (Note: Anisotropic Pressure Coupling)' + name: 'Gromos 43A1-S3 Pope Simulations (Versions 1 And 2) 313 K (Note: Anisotropic + Pressure Coupling)' publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/f7f/cf7/f7fcf7af39e28aa50b5c6451e464dddb0a5bca16/436d42e44cdadef6bf70834b96936b1f71baecf2/README.yaml b/Simulations/f7f/cf7/f7fcf7af39e28aa50b5c6451e464dddb0a5bca16/436d42e44cdadef6bf70834b96936b1f71baecf2/README.yaml index f7f55e15cd..58da5504ef 100644 --- a/Simulations/f7f/cf7/f7fcf7af39e28aa50b5c6451e464dddb0a5bca16/436d42e44cdadef6bf70834b96936b1f71baecf2/README.yaml +++ b/Simulations/f7f/cf7/f7fcf7af39e28aa50b5c6451e464dddb0a5bca16/436d42e44cdadef6bf70834b96936b1f71baecf2/README.yaml @@ -49,9 +49,14 @@ SOFTWARE: gromacs DIR_WRK: /usr/home/bort/Databank ID: 282 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL (48:35:17) bilayer at 310 K (Slipids for lipids, Kohagen for CaCl_2, GROMACS 4.6, 100 ns) [NMRlipids simulation 282] + name: Molecular dynamics trajectory of a POPC/CLA/CAL (48:35:17) bilayer at 310 + K (Slipids for lipids, Kohagen for CaCl_2, GROMACS 4.6, 100 ns) [NMRlipids simulation + 282] alternateName: 200POPC_9000SOL_73CAL_146CLA_310K_ECC-scaled ions - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 48 mol%), 146 CLA (35 mol%) and 73 CAL (17 mol%) at 310 K. Simulated with Slipids for lipids, Kohagen for CaCl_2 in GROMACS 4.6 for 100 ns (54019 atoms). Deposited as NMRlipids Databank simulation 282 and available from https://doi.org/10.5281/zenodo.45007. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 48 mol%), 146 CLA (35 mol%) and 73 CAL (17 mol%) at 310 K. Simulated with Slipids + for lipids, Kohagen for CaCl_2 in GROMACS 4.6 for 100 ns (54019 atoms). Deposited + as NMRlipids Databank simulation 282 and available from https://doi.org/10.5281/zenodo.45007. sameAs: https://doi.org/10.5281/zenodo.45007 datePublished: '2016-01-19' license: diff --git a/Simulations/f83/806/f83806c3a0af6edc5b32cd7769ac7e689b4c5331/f0ccd45496dd8a2bb993c75e728bac817cf3bae8/README.yaml b/Simulations/f83/806/f83806c3a0af6edc5b32cd7769ac7e689b4c5331/f0ccd45496dd8a2bb993c75e728bac817cf3bae8/README.yaml index 8561aae6e5..a6df28cc1d 100644 --- a/Simulations/f83/806/f83806c3a0af6edc5b32cd7769ac7e689b4c5331/f0ccd45496dd8a2bb993c75e728bac817cf3bae8/README.yaml +++ b/Simulations/f83/806/f83806c3a0af6edc5b32cd7769ac7e689b4c5331/f0ccd45496dd8a2bb993c75e728bac817cf3bae8/README.yaml @@ -64,9 +64,14 @@ WARNINGS: ORIENTATION: x-normal ID: 487 bioschema_properties: - name: Molecular dynamics trajectory of a DPPC/DOPC/CHOL/CLA/SOD (40:32:10:9:9) bilayer at 293 K (Slipids, GROMACS, 600 ns) [NMRlipids simulation 487] + name: Molecular dynamics trajectory of a DPPC/DOPC/CHOL/CLA/SOD (40:32:10:9:9) bilayer + at 293 K (Slipids, GROMACS, 600 ns) [NMRlipids simulation 487] alternateName: 204DPPC_52CHOL_166DOPC_16880SOL_46SOD_46CLA_293K - description: Molecular dynamics trajectory of a lipid bilayer of 204 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 40 mol%), 166 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, 32 mol%), 52 CHOL (cholesterol, 10 mol%), 46 CLA (9 mol%) and 46 SOD (9 mol%) at 293 K. Simulated with Slipids in GROMACS for 600 ns (104008 atoms). Deposited as NMRlipids Databank simulation 487 and available from https://doi.org/10.5281/zenodo.3540513. + description: Molecular dynamics trajectory of a lipid bilayer of 204 DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, + 40 mol%), 166 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, 32 mol%), 52 CHOL + (cholesterol, 10 mol%), 46 CLA (9 mol%) and 46 SOD (9 mol%) at 293 K. Simulated + with Slipids in GROMACS for 600 ns (104008 atoms). Deposited as NMRlipids Databank + simulation 487 and available from https://doi.org/10.5281/zenodo.3540513. sameAs: https://doi.org/10.5281/zenodo.3540513 datePublished: '2019-11-13' license: diff --git a/Simulations/f8a/f16/f8af169dd74cbbb67247869c50483ba94767b62c/6780b9a6f2f5bd0ac45772065f9b022fa67bfbff/README.yaml b/Simulations/f8a/f16/f8af169dd74cbbb67247869c50483ba94767b62c/6780b9a6f2f5bd0ac45772065f9b022fa67bfbff/README.yaml index c4af767a92..841339f225 100644 --- a/Simulations/f8a/f16/f8af169dd74cbbb67247869c50483ba94767b62c/6780b9a6f2f5bd0ac45772065f9b022fa67bfbff/README.yaml +++ b/Simulations/f8a/f16/f8af169dd74cbbb67247869c50483ba94767b62c/6780b9a6f2f5bd0ac45772065f9b022fa67bfbff/README.yaml @@ -46,9 +46,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 808 bioschema_properties: - name: Molecular dynamics trajectory of a DMPC bilayer at 314 K (CHARMM36, GROMACS 2022.2, 500 ns) [NMRlipids simulation 808] + name: Molecular dynamics trajectory of a DMPC bilayer at 314 K (CHARMM36, GROMACS + 2022.2, 500 ns) [NMRlipids simulation 808] alternateName: 200DMPC_10kSOL_300K - description: Molecular dynamics trajectory of a lipid bilayer of 200 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) at 314 K. Simulated with CHARMM36 in GROMACS 2022.2 for 500 ns (53600 atoms). Deposited as NMRlipids Databank simulation 808 and available from https://doi.org/10.5281/zenodo.10949663. + description: Molecular dynamics trajectory of a lipid bilayer of 200 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) + at 314 K. Simulated with CHARMM36 in GROMACS 2022.2 for 500 ns (53600 atoms). + Deposited as NMRlipids Databank simulation 808 and available from https://doi.org/10.5281/zenodo.10949663. sameAs: https://doi.org/10.5281/zenodo.10949663 datePublished: '2024-04-09' license: diff --git a/Simulations/f97/dff/f97dfff6e14f18c3d24bda5b8fdf9d4b4a7ec763/d9fa5dfeae8940ba2ee2faa7784bec5b2d44613a/README.yaml b/Simulations/f97/dff/f97dfff6e14f18c3d24bda5b8fdf9d4b4a7ec763/d9fa5dfeae8940ba2ee2faa7784bec5b2d44613a/README.yaml index e6506ca884..affdd42192 100644 --- a/Simulations/f97/dff/f97dfff6e14f18c3d24bda5b8fdf9d4b4a7ec763/d9fa5dfeae8940ba2ee2faa7784bec5b2d44613a/README.yaml +++ b/Simulations/f97/dff/f97dfff6e14f18c3d24bda5b8fdf9d4b4a7ec763/d9fa5dfeae8940ba2ee2faa7784bec5b2d44613a/README.yaml @@ -64,9 +64,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 120 bioschema_properties: - name: Molecular dynamics trajectory of a CLA/DMPC/DMTAP/SOD (39:22:22:17) bilayer at 323 K (Berger with DMTAP modification by Gurtovenko et al., GROMACS 3.x, 179 ns) [NMRlipids simulation 120] + name: Molecular dynamics trajectory of a CLA/DMPC/DMTAP/SOD (39:22:22:17) bilayer + at 323 K (Berger with DMTAP modification by Gurtovenko et al., GROMACS 3.x, 179 + ns) [NMRlipids simulation 120] alternateName: 64DMPC_64DMTAP_48SOD_112CLA_5240SOL_323K - description: Molecular dynamics trajectory of a lipid bilayer of 112 CLA (39 mol%), 64 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine, 22 mol%), 64 DMTAP (1,2-dimyristoyl-3-trimethylammonium-propane, 22 mol%) and 48 SOD (17 mol%) at 323 K. Simulated with Berger with DMTAP modification by Gurtovenko et al. in GROMACS 3.x for 179 ns (21320 atoms). Deposited as NMRlipids Databank simulation 120 and available from https://doi.org/10.5281/zenodo.53151. + description: Molecular dynamics trajectory of a lipid bilayer of 112 CLA (39 mol%), + 64 DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine, 22 mol%), 64 DMTAP (1,2-dimyristoyl-3-trimethylammonium-propane, + 22 mol%) and 48 SOD (17 mol%) at 323 K. Simulated with Berger with DMTAP modification + by Gurtovenko et al. in GROMACS 3.x for 179 ns (21320 atoms). Deposited as NMRlipids + Databank simulation 120 and available from https://doi.org/10.5281/zenodo.53151. sameAs: https://doi.org/10.5281/zenodo.53151 datePublished: '2016-05-26' license: @@ -165,7 +171,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.53151 identifier: 10.5281/zenodo.53151 url: https://doi.org/10.5281/zenodo.53151 - name: 'Molecular dynamics simulation trajectory of a cationic lipid bilayer: 50/50 mol% DMTAP/DMPC in 0.5 M NaCl' + name: 'Molecular dynamics simulation trajectory of a cationic lipid bilayer: 50/50 + mol% DMTAP/DMPC in 0.5 M NaCl' publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/f9e/feb/f9efeb63d3508da7db711ba4a338390a81ab2f16/17ceae0ed2c39e9dc605abcdabf84cb40f398b09/README.yaml b/Simulations/f9e/feb/f9efeb63d3508da7db711ba4a338390a81ab2f16/17ceae0ed2c39e9dc605abcdabf84cb40f398b09/README.yaml index 287beefdae..563e3b88f6 100644 --- a/Simulations/f9e/feb/f9efeb63d3508da7db711ba4a338390a81ab2f16/17ceae0ed2c39e9dc605abcdabf84cb40f398b09/README.yaml +++ b/Simulations/f9e/feb/f9efeb63d3508da7db711ba4a338390a81ab2f16/17ceae0ed2c39e9dc605abcdabf84cb40f398b09/README.yaml @@ -50,9 +50,13 @@ SOFTWARE: gromacs DIR_WRK: /usr/home/bort/Databank ID: 135 bioschema_properties: - name: Molecular dynamics trajectory of a DAPC/CHOL (90:10) bilayer at 298 K (CHARMM36, GROMACS, 1000 ns) [NMRlipids simulation 135] + name: Molecular dynamics trajectory of a DAPC/CHOL (90:10) bilayer at 298 K (CHARMM36, + GROMACS, 1000 ns) [NMRlipids simulation 135] alternateName: 260DAPC_28CHOL_11520SOL_298K - description: Molecular dynamics trajectory of a lipid bilayer of 260 DAPC (1,2-diarachidonoyl-sn-glycero-3-phosphocholine, 90 mol%) and 28 CHOL (cholesterol, 10 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for 1000 ns (72512 atoms). Deposited as NMRlipids Databank simulation 135 and available from https://doi.org/10.5281/zenodo.2653721. + description: Molecular dynamics trajectory of a lipid bilayer of 260 DAPC (1,2-diarachidonoyl-sn-glycero-3-phosphocholine, + 90 mol%) and 28 CHOL (cholesterol, 10 mol%) at 298 K. Simulated with CHARMM36 + in GROMACS for 1000 ns (72512 atoms). Deposited as NMRlipids Databank simulation + 135 and available from https://doi.org/10.5281/zenodo.2653721. sameAs: https://doi.org/10.5281/zenodo.2653721 datePublished: '2019-04-29' license: @@ -141,7 +145,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.2653721 identifier: 10.5281/zenodo.2653721 url: https://doi.org/10.5281/zenodo.2653721 - name: Atomistic simulations of cholesterol in symmetric lipid bilayers with varying degrees of lipid chain unsaturation + name: Atomistic simulations of cholesterol in symmetric lipid bilayers with varying + degrees of lipid chain unsaturation publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/fa3/458/fa34583fd2a80ef3717ab05ae626fb4abdcbad44/2be9688985eb0b9fa11cec7b6ba8a674181aa21a/README.yaml b/Simulations/fa3/458/fa34583fd2a80ef3717ab05ae626fb4abdcbad44/2be9688985eb0b9fa11cec7b6ba8a674181aa21a/README.yaml index d78a02f889..401b9d3c18 100644 --- a/Simulations/fa3/458/fa34583fd2a80ef3717ab05ae626fb4abdcbad44/2be9688985eb0b9fa11cec7b6ba8a674181aa21a/README.yaml +++ b/Simulations/fa3/458/fa34583fd2a80ef3717ab05ae626fb4abdcbad44/2be9688985eb0b9fa11cec7b6ba8a674181aa21a/README.yaml @@ -55,9 +55,14 @@ TRJ: DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 368 bioschema_properties: - name: Molecular dynamics trajectory of a CLA/CAL/POPC/POPG/SOD (48:24:19:5:5) bilayer at 298 K (CHARMM36, GROMACS, 289 ns) [NMRlipids simulation 368] + name: Molecular dynamics trajectory of a CLA/CAL/POPC/POPG/SOD (48:24:19:5:5) bilayer + at 298 K (CHARMM36, GROMACS, 289 ns) [NMRlipids simulation 368] alternateName: POPC:POPG(4:1)+1MCaCl_T298K - description: Molecular dynamics trajectory of a lipid bilayer of 902 CLA (48 mol%), 451 CAL (24 mol%), 350 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 19 mol%), 88 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 5 mol%) and 88 SOD (5 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for 289 ns (134298 atoms). Deposited as NMRlipids Databank simulation 368 and available from https://doi.org/10.5281/zenodo.3997037. + description: Molecular dynamics trajectory of a lipid bilayer of 902 CLA (48 mol%), + 451 CAL (24 mol%), 350 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 19 mol%), 88 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 5 mol%) + and 88 SOD (5 mol%) at 298 K. Simulated with CHARMM36 in GROMACS for 289 ns (134298 + atoms). Deposited as NMRlipids Databank simulation 368 and available from https://doi.org/10.5281/zenodo.3997037. sameAs: https://doi.org/10.5281/zenodo.3997037 datePublished: '2020-08-24' license: @@ -147,7 +152,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3997037 identifier: 10.5281/zenodo.3997037 url: https://doi.org/10.5281/zenodo.3997037 - name: POPC:POPG 4:1 MD simulation with CHARMM36 in 1 M CaCL2 solution with Na+ counterions + name: POPC:POPG 4:1 MD simulation with CHARMM36 in 1 M CaCL2 solution with Na+ + counterions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/fa5/56d/fa556d103c86221ef1a71462cb1743390a50c44e/00c6afcc95e6f22f7d1722cf0d06c91324e8bb70/README.yaml b/Simulations/fa5/56d/fa556d103c86221ef1a71462cb1743390a50c44e/00c6afcc95e6f22f7d1722cf0d06c91324e8bb70/README.yaml index 4418347d4e..76d1626ebb 100644 --- a/Simulations/fa5/56d/fa556d103c86221ef1a71462cb1743390a50c44e/00c6afcc95e6f22f7d1722cf0d06c91324e8bb70/README.yaml +++ b/Simulations/fa5/56d/fa556d103c86221ef1a71462cb1743390a50c44e/00c6afcc95e6f22f7d1722cf0d06c91324e8bb70/README.yaml @@ -51,9 +51,13 @@ EXPERIMENT: CHOL: [] FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a DOPC/CHOL (89:11) bilayer at 333.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 650] + name: Molecular dynamics trajectory of a DOPC/CHOL (89:11) bilayer at 333.15 K (CHARMM36, + GROMACS, 1001 ns) [NMRlipids simulation 650] alternateName: 1024DOPC_128CHOL_57600SOL_333K - description: Molecular dynamics trajectory of a lipid bilayer of 1024 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, 89 mol%) and 128 CHOL (cholesterol, 11 mol%) at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (323584 atoms). Deposited as NMRlipids Databank simulation 650 and available from https://doi.org/10.5281/zenodo.6943929. + description: Molecular dynamics trajectory of a lipid bilayer of 1024 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine, + 89 mol%) and 128 CHOL (cholesterol, 11 mol%) at 333.15 K. Simulated with CHARMM36 + in GROMACS for 1001 ns (323584 atoms). Deposited as NMRlipids Databank simulation + 650 and available from https://doi.org/10.5281/zenodo.6943929. sameAs: https://doi.org/10.5281/zenodo.6943929 datePublished: '2022-07-30' license: diff --git a/Simulations/fa8/3ff/fa83ff3ab50fb1be21d7c78de12363d512678601/77a52c813f14174610eed414fa0504b0d1efbeea/README.yaml b/Simulations/fa8/3ff/fa83ff3ab50fb1be21d7c78de12363d512678601/77a52c813f14174610eed414fa0504b0d1efbeea/README.yaml index 8525736b4c..2a35561a88 100644 --- a/Simulations/fa8/3ff/fa83ff3ab50fb1be21d7c78de12363d512678601/77a52c813f14174610eed414fa0504b0d1efbeea/README.yaml +++ b/Simulations/fa8/3ff/fa83ff3ab50fb1be21d7c78de12363d512678601/77a52c813f14174610eed414fa0504b0d1efbeea/README.yaml @@ -50,9 +50,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 2 bioschema_properties: - name: Molecular dynamics trajectory of a DAPC/CHOL (90:10) bilayer at 333 K (CHARMM36, GROMACS, 2000 ns) [NMRlipids simulation 2] + name: Molecular dynamics trajectory of a DAPC/CHOL (90:10) bilayer at 333 K (CHARMM36, + GROMACS, 2000 ns) [NMRlipids simulation 2] alternateName: 260DAPC_28CHOL_11520SOL_333K - description: Molecular dynamics trajectory of a lipid bilayer of 260 DAPC (1,2-diarachidonoyl-sn-glycero-3-phosphocholine, 90 mol%) and 28 CHOL (cholesterol, 10 mol%) at 333 K. Simulated with CHARMM36 in GROMACS for 2000 ns (72512 atoms). Deposited as NMRlipids Databank simulation 2 and available from https://doi.org/10.5281/zenodo.2653735. + description: Molecular dynamics trajectory of a lipid bilayer of 260 DAPC (1,2-diarachidonoyl-sn-glycero-3-phosphocholine, + 90 mol%) and 28 CHOL (cholesterol, 10 mol%) at 333 K. Simulated with CHARMM36 + in GROMACS for 2000 ns (72512 atoms). Deposited as NMRlipids Databank simulation + 2 and available from https://doi.org/10.5281/zenodo.2653735. sameAs: https://doi.org/10.5281/zenodo.2653735 datePublished: '2019-04-29' license: @@ -141,7 +145,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.2653735 identifier: 10.5281/zenodo.2653735 url: https://doi.org/10.5281/zenodo.2653735 - name: Atomistic simulations of DAPC/cholesterol bilayers with one cholesterol restrained to the membrane core + name: Atomistic simulations of DAPC/cholesterol bilayers with one cholesterol + restrained to the membrane core publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/fb8/2e4/fb82e4f256fd9c13a9a29a32fbd1f9a8d2191ef6/fb82e4f256fd9c13a9a29a32fbd1f9a8d2191ef6/README.yaml b/Simulations/fb8/2e4/fb82e4f256fd9c13a9a29a32fbd1f9a8d2191ef6/fb82e4f256fd9c13a9a29a32fbd1f9a8d2191ef6/README.yaml index f4cab22a5e..4622815248 100644 --- a/Simulations/fb8/2e4/fb82e4f256fd9c13a9a29a32fbd1f9a8d2191ef6/fb82e4f256fd9c13a9a29a32fbd1f9a8d2191ef6/README.yaml +++ b/Simulations/fb8/2e4/fb82e4f256fd9c13a9a29a32fbd1f9a8d2191ef6/fb82e4f256fd9c13a9a29a32fbd1f9a8d2191ef6/README.yaml @@ -40,9 +40,12 @@ EXPERIMENT: FORMFACTOR: - 10.1016/j.bbamem.2011.07.022/2 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 303 K (Charmm-Drude polarizable, OPENMM, 200 ns) [NMRlipids simulation 749] + name: Molecular dynamics trajectory of a POPC bilayer at 303 K (Charmm-Drude polarizable, + OPENMM, 200 ns) [NMRlipids simulation 749] alternateName: POPC_CHARMMdrude2023_303K - description: Molecular dynamics trajectory of a lipid bilayer of 72 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 303 K. Simulated with Charmm-Drude polarizable in OPENMM for 200 ns (25163 atoms). Deposited as NMRlipids Databank simulation 749 and available from https://doi.org/10.5281/zenodo.7916287. + description: Molecular dynamics trajectory of a lipid bilayer of 72 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 303 K. Simulated with Charmm-Drude polarizable in OPENMM for 200 ns (25163 + atoms). Deposited as NMRlipids Databank simulation 749 and available from https://doi.org/10.5281/zenodo.7916287. sameAs: https://doi.org/10.5281/zenodo.7916287 datePublished: '2023-05-09' license: @@ -130,7 +133,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.7916287 identifier: 10.5281/zenodo.7916287 url: https://doi.org/10.5281/zenodo.7916287 - name: OpenMM simulations of POPC using the CHARMM Drude2023 force field in xtc format + name: OpenMM simulations of POPC using the CHARMM Drude2023 force field in xtc + format publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/fb9/921/fb992117655d3e932d60fea4a33002809c343f68/e360213ebfab74525db2ea2b13137c8f41cb5a30/README.yaml b/Simulations/fb9/921/fb992117655d3e932d60fea4a33002809c343f68/e360213ebfab74525db2ea2b13137c8f41cb5a30/README.yaml index 99c0982e93..af0b259531 100644 --- a/Simulations/fb9/921/fb992117655d3e932d60fea4a33002809c343f68/e360213ebfab74525db2ea2b13137c8f41cb5a30/README.yaml +++ b/Simulations/fb9/921/fb992117655d3e932d60fea4a33002809c343f68/e360213ebfab74525db2ea2b13137c8f41cb5a30/README.yaml @@ -49,9 +49,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 709 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (71:29) bilayer at 298.15 K (Slipids, GROMACS 2021, 1001 ns) [NMRlipids simulation 709] + name: Molecular dynamics trajectory of a POPC/CHOL (71:29) bilayer at 298.15 K (Slipids, + GROMACS 2021, 1001 ns) [NMRlipids simulation 709] alternateName: Slipids_POPC_CHOL29_L - description: Molecular dynamics trajectory of a lipid bilayer of 1024 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 71 mol%) and 416 CHOL (cholesterol, 29 mol%) at 298.15 K. Simulated with Slipids in GROMACS 2021 for 1001 ns (384000 atoms). Deposited as NMRlipids Databank simulation 709 and available from https://doi.org/10.5281/zenodo.7022749. + description: Molecular dynamics trajectory of a lipid bilayer of 1024 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 71 mol%) and 416 CHOL (cholesterol, 29 mol%) at 298.15 K. Simulated with Slipids + in GROMACS 2021 for 1001 ns (384000 atoms). Deposited as NMRlipids Databank simulation + 709 and available from https://doi.org/10.5281/zenodo.7022749. sameAs: https://doi.org/10.5281/zenodo.7022749 datePublished: '2022-08-23' license: diff --git a/Simulations/fb9/c8d/fb9c8d1e7ff7d08126c4ab7bb2ccbc55b6093afe/4eb4b693bb11fc8b6183f88f0f98f594c9348e3e/README.yaml b/Simulations/fb9/c8d/fb9c8d1e7ff7d08126c4ab7bb2ccbc55b6093afe/4eb4b693bb11fc8b6183f88f0f98f594c9348e3e/README.yaml index 8f726e85ce..aad1c24f5f 100644 --- a/Simulations/fb9/c8d/fb9c8d1e7ff7d08126c4ab7bb2ccbc55b6093afe/4eb4b693bb11fc8b6183f88f0f98f594c9348e3e/README.yaml +++ b/Simulations/fb9/c8d/fb9c8d1e7ff7d08126c4ab7bb2ccbc55b6093afe/4eb4b693bb11fc8b6183f88f0f98f594c9348e3e/README.yaml @@ -41,9 +41,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 452 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 310 K (MacRog, GROMACS 4.6, 500 ns) [NMRlipids simulation 452] + name: Molecular dynamics trajectory of a POPC bilayer at 310 K (MacRog, GROMACS + 4.6, 500 ns) [NMRlipids simulation 452] alternateName: 128POPC_6400SOL_310K - description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 310 K. Simulated with MacRog in GROMACS 4.6 for 500 ns (36352 atoms). Deposited as NMRlipids Databank simulation 452 and available from https://doi.org/10.5281/zenodo.3252052. + description: Molecular dynamics trajectory of a lipid bilayer of 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 310 K. Simulated with MacRog in GROMACS 4.6 for 500 ns (36352 atoms). Deposited + as NMRlipids Databank simulation 452 and available from https://doi.org/10.5281/zenodo.3252052. sameAs: https://doi.org/10.5281/zenodo.3252052 datePublished: '2015-01-11' license: @@ -134,7 +137,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.3252052 identifier: 10.5281/zenodo.3252052 url: https://doi.org/10.5281/zenodo.3252052 - name: POPC/Cholesterol @ 310K. 0, 10, 40, 50 and 60 mol-% cholesterol. Model by Maciejewski and Rog + name: POPC/Cholesterol @ 310K. 0, 10, 40, 50 and 60 mol-% cholesterol. Model by + Maciejewski and Rog publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/fbe/a98/fbea988ad404d7791ce502562a9195acaddc9247/0f475e1b3dcbe493d3852d2c6109766129db6865/README.yaml b/Simulations/fbe/a98/fbea988ad404d7791ce502562a9195acaddc9247/0f475e1b3dcbe493d3852d2c6109766129db6865/README.yaml index bf0140e9f9..c6a93d6277 100644 --- a/Simulations/fbe/a98/fbea988ad404d7791ce502562a9195acaddc9247/0f475e1b3dcbe493d3852d2c6109766129db6865/README.yaml +++ b/Simulations/fbe/a98/fbea988ad404d7791ce502562a9195acaddc9247/0f475e1b3dcbe493d3852d2c6109766129db6865/README.yaml @@ -48,9 +48,13 @@ SOFTWARE: gromacs DIR_WRK: /usr/home/bort/Databank ID: 466 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (82:9:9) bilayer at 310 K (CHARMM36, GROMACS 2016.1, 4178 ns) [NMRlipids simulation 466] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (82:9:9) bilayer at 310 K + (CHARMM36, GROMACS 2016.1, 4178 ns) [NMRlipids simulation 466] alternateName: 512POPC_20480SOL_55SOD_55CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 512 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 82 mol%), 55 CLA (9 mol%) and 55 SOD (9 mol%) at 310 K. Simulated with CHARMM36 in GROMACS 2016.1 for 4178 ns (130158 atoms). Deposited as NMRlipids Databank simulation 466 and available from https://doi.org/10.5281/zenodo.3228177. + description: Molecular dynamics trajectory of a lipid bilayer of 512 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 82 mol%), 55 CLA (9 mol%) and 55 SOD (9 mol%) at 310 K. Simulated with CHARMM36 + in GROMACS 2016.1 for 4178 ns (130158 atoms). Deposited as NMRlipids Databank + simulation 466 and available from https://doi.org/10.5281/zenodo.3228177. sameAs: https://doi.org/10.5281/zenodo.3228177 datePublished: '2019-05-28' license: diff --git a/Simulations/fbe/a98/fbea988ad404d7791ce502562a9195acaddc9247/b7307dfec8690349ee5ca975e8739df7a0a920c5/README.yaml b/Simulations/fbe/a98/fbea988ad404d7791ce502562a9195acaddc9247/b7307dfec8690349ee5ca975e8739df7a0a920c5/README.yaml index 36c3605e3e..7b75b0c60a 100644 --- a/Simulations/fbe/a98/fbea988ad404d7791ce502562a9195acaddc9247/b7307dfec8690349ee5ca975e8739df7a0a920c5/README.yaml +++ b/Simulations/fbe/a98/fbea988ad404d7791ce502562a9195acaddc9247/b7307dfec8690349ee5ca975e8739df7a0a920c5/README.yaml @@ -50,9 +50,13 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 467 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (82:9:9) bilayer at 310 K (CHARMM36, GROMACS 5.0.4, 500 ns) [NMRlipids simulation 467] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (82:9:9) bilayer at 310 K + (CHARMM36, GROMACS 5.0.4, 500 ns) [NMRlipids simulation 467] alternateName: 512POPC_20480SOL_55SOD_55CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 512 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 82 mol%), 55 CLA (9 mol%) and 55 SOD (9 mol%) at 310 K. Simulated with CHARMM36 in GROMACS 5.0.4 for 500 ns (130158 atoms). Deposited as NMRlipids Databank simulation 467 and available from https://doi.org/10.5281/zenodo.1010083. + description: Molecular dynamics trajectory of a lipid bilayer of 512 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 82 mol%), 55 CLA (9 mol%) and 55 SOD (9 mol%) at 310 K. Simulated with CHARMM36 + in GROMACS 5.0.4 for 500 ns (130158 atoms). Deposited as NMRlipids Databank simulation + 467 and available from https://doi.org/10.5281/zenodo.1010083. sameAs: https://doi.org/10.5281/zenodo.1010083 datePublished: '2017-10-12' license: diff --git a/Simulations/fbe/d55/fbed55ebb58b32963a3e1c4a94aee9c12304ce9e/af523346e81b780e2e01b1253219c1f03d5dd731/README.yaml b/Simulations/fbe/d55/fbed55ebb58b32963a3e1c4a94aee9c12304ce9e/af523346e81b780e2e01b1253219c1f03d5dd731/README.yaml index a9d98a8902..8ae34f5c69 100644 --- a/Simulations/fbe/d55/fbed55ebb58b32963a3e1c4a94aee9c12304ce9e/af523346e81b780e2e01b1253219c1f03d5dd731/README.yaml +++ b/Simulations/fbe/d55/fbed55ebb58b32963a3e1c4a94aee9c12304ce9e/af523346e81b780e2e01b1253219c1f03d5dd731/README.yaml @@ -45,9 +45,12 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/1 ID: 710 bioschema_properties: - name: Molecular dynamics trajectory of a POPC bilayer at 298.15 K (CHARMM36, GROMACS 2021, 1001 ns) [NMRlipids simulation 710] + name: Molecular dynamics trajectory of a POPC bilayer at 298.15 K (CHARMM36, GROMACS + 2021, 1001 ns) [NMRlipids simulation 710] alternateName: POPC_M - description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) at 298.15 K. Simulated with CHARMM36 in GROMACS 2021 for 1001 ns (72704 atoms). Deposited as NMRlipids Databank simulation 710 and available from https://doi.org/10.5281/zenodo.7103807. + description: Molecular dynamics trajectory of a lipid bilayer of 256 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) + at 298.15 K. Simulated with CHARMM36 in GROMACS 2021 for 1001 ns (72704 atoms). + Deposited as NMRlipids Databank simulation 710 and available from https://doi.org/10.5281/zenodo.7103807. sameAs: https://doi.org/10.5281/zenodo.7103807 datePublished: '2022-09-22' license: diff --git a/Simulations/fc6/4cf/fc64cfa660ee70c03a351a8fc85eb1984530772a/74a5730870f5a5131977cb550c65031e7f85f0ea/README.yaml b/Simulations/fc6/4cf/fc64cfa660ee70c03a351a8fc85eb1984530772a/74a5730870f5a5131977cb550c65031e7f85f0ea/README.yaml index e712ffc1de..085c6a5106 100644 --- a/Simulations/fc6/4cf/fc64cfa660ee70c03a351a8fc85eb1984530772a/74a5730870f5a5131977cb550c65031e7f85f0ea/README.yaml +++ b/Simulations/fc6/4cf/fc64cfa660ee70c03a351a8fc85eb1984530772a/74a5730870f5a5131977cb550c65031e7f85f0ea/README.yaml @@ -54,9 +54,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 450 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/DHMDMAB (54:23:23) bilayer at 313 K (Lipid14, GROMACS, 80 ns) [NMRlipids simulation 450] + name: Molecular dynamics trajectory of a POPC/CLA/DHMDMAB (54:23:23) bilayer at + 313 K (Lipid14, GROMACS, 80 ns) [NMRlipids simulation 450] alternateName: 100POPC_42DHMDMAB_6214SOL_42CLA_313K - description: Molecular dynamics trajectory of a lipid bilayer of 100 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 54 mol%), 42 CLA (23 mol%) and 42 DHMDMAB (dihexadecyldimethylammonium, 23 mol%) at 313 K. Simulated with Lipid14 in GROMACS for 80 ns (36578 atoms). Deposited as NMRlipids Databank simulation 450 and available from https://doi.org/10.5281/zenodo.1020623. + description: Molecular dynamics trajectory of a lipid bilayer of 100 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 54 mol%), 42 CLA (23 mol%) and 42 DHMDMAB (dihexadecyldimethylammonium, 23 mol%) + at 313 K. Simulated with Lipid14 in GROMACS for 80 ns (36578 atoms). Deposited + as NMRlipids Databank simulation 450 and available from https://doi.org/10.5281/zenodo.1020623. sameAs: https://doi.org/10.5281/zenodo.1020623 datePublished: '2017-10-18' license: @@ -145,7 +149,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1020623 identifier: 10.5281/zenodo.1020623 url: https://doi.org/10.5281/zenodo.1020623 - name: Popc Bilayer With 30% Of Dihexadecyldimethylammonium Simulated At T313K With The Lipid14 Model Using Gromacs + name: Popc Bilayer With 30% Of Dihexadecyldimethylammonium Simulated At T313K + With The Lipid14 Model Using Gromacs publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/fc9/adc/fc9adc57cdc847019621267bfed6cc71d05d93a7/cddacbf14fa088499729ab009228a3d6f25b38ea/README.yaml b/Simulations/fc9/adc/fc9adc57cdc847019621267bfed6cc71d05d93a7/cddacbf14fa088499729ab009228a3d6f25b38ea/README.yaml index e92d2d26e6..74e2014b76 100644 --- a/Simulations/fc9/adc/fc9adc57cdc847019621267bfed6cc71d05d93a7/cddacbf14fa088499729ab009228a3d6f25b38ea/README.yaml +++ b/Simulations/fc9/adc/fc9adc57cdc847019621267bfed6cc71d05d93a7/cddacbf14fa088499729ab009228a3d6f25b38ea/README.yaml @@ -55,9 +55,13 @@ EXPERIMENT: FORMFACTOR: [] ID: 523 bioschema_properties: - name: Molecular dynamics trajectory of a CLA/POPC/CAL (48:28:24) bilayer at 313 K (ECC-lipids, GROMACS 5.1.4, 300 ns) [NMRlipids simulation 523] + name: Molecular dynamics trajectory of a CLA/POPC/CAL (48:28:24) bilayer at 313 + K (ECC-lipids, GROMACS 5.1.4, 300 ns) [NMRlipids simulation 523] alternateName: 128POPC_6232SOL_110CAL_220CLA_313K_TIP4p2005model - description: Molecular dynamics trajectory of a lipid bilayer of 220 CLA (48 mol%), 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 28 mol%) and 110 CAL (24 mol%) at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 300 ns (42410 atoms). Deposited as NMRlipids Databank simulation 523 and available from https://doi.org/10.5281/zenodo.1118980. + description: Molecular dynamics trajectory of a lipid bilayer of 220 CLA (48 mol%), + 128 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 28 mol%) and 110 CAL + (24 mol%) at 313 K. Simulated with ECC-lipids in GROMACS 5.1.4 for 300 ns (42410 + atoms). Deposited as NMRlipids Databank simulation 523 and available from https://doi.org/10.5281/zenodo.1118980. sameAs: https://doi.org/10.5281/zenodo.1118980 datePublished: '2017-12-19' license: @@ -147,7 +151,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1118980 identifier: 10.5281/zenodo.1118980 url: https://doi.org/10.5281/zenodo.1118980 - name: Simulations Of Popc Lipid Bilayer In Water Solution At Various Nacl And Cacl2 Concentrations Using Ecc-Popc Force Field And Various Water Models + name: Simulations Of Popc Lipid Bilayer In Water Solution At Various Nacl And + Cacl2 Concentrations Using Ecc-Popc Force Field And Various Water Models publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/fce/b36/fceb361ce5ba5115f78ecaae22ead1a2149ddb38/f9a0fd9eb641aa524d32def10e2bc8eb2ef1f4e8/README.yaml b/Simulations/fce/b36/fceb361ce5ba5115f78ecaae22ead1a2149ddb38/f9a0fd9eb641aa524d32def10e2bc8eb2ef1f4e8/README.yaml index 06574d0e03..72fab8ff3b 100644 --- a/Simulations/fce/b36/fceb361ce5ba5115f78ecaae22ead1a2149ddb38/f9a0fd9eb641aa524d32def10e2bc8eb2ef1f4e8/README.yaml +++ b/Simulations/fce/b36/fceb361ce5ba5115f78ecaae22ead1a2149ddb38/f9a0fd9eb641aa524d32def10e2bc8eb2ef1f4e8/README.yaml @@ -50,9 +50,13 @@ SOFTWARE: gromacs DIR_WRK: /usr/home/bort/Databank ID: 34 bioschema_properties: - name: Molecular dynamics trajectory of a DAPC/CHOL (90:10) bilayer at 310 K (CHARMM36, GROMACS, 1000 ns) [NMRlipids simulation 34] + name: Molecular dynamics trajectory of a DAPC/CHOL (90:10) bilayer at 310 K (CHARMM36, + GROMACS, 1000 ns) [NMRlipids simulation 34] alternateName: 260DAPC_28CHOL_11520SOL_310K - description: Molecular dynamics trajectory of a lipid bilayer of 260 DAPC (1,2-diarachidonoyl-sn-glycero-3-phosphocholine, 90 mol%) and 28 CHOL (cholesterol, 10 mol%) at 310 K. Simulated with CHARMM36 in GROMACS for 1000 ns (72512 atoms). Deposited as NMRlipids Databank simulation 34 and available from https://doi.org/10.5281/zenodo.2653721. + description: Molecular dynamics trajectory of a lipid bilayer of 260 DAPC (1,2-diarachidonoyl-sn-glycero-3-phosphocholine, + 90 mol%) and 28 CHOL (cholesterol, 10 mol%) at 310 K. Simulated with CHARMM36 + in GROMACS for 1000 ns (72512 atoms). Deposited as NMRlipids Databank simulation + 34 and available from https://doi.org/10.5281/zenodo.2653721. sameAs: https://doi.org/10.5281/zenodo.2653721 datePublished: '2019-04-29' license: @@ -141,7 +145,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.2653721 identifier: 10.5281/zenodo.2653721 url: https://doi.org/10.5281/zenodo.2653721 - name: Atomistic simulations of cholesterol in symmetric lipid bilayers with varying degrees of lipid chain unsaturation + name: Atomistic simulations of cholesterol in symmetric lipid bilayers with varying + degrees of lipid chain unsaturation publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/fd2/138/fd2138f941c9231f458679767081d36f8755fe7d/96cc0e7df5b0a0336bffb06345e68c98849772e8/README.yaml b/Simulations/fd2/138/fd2138f941c9231f458679767081d36f8755fe7d/96cc0e7df5b0a0336bffb06345e68c98849772e8/README.yaml index fdf5e0548d..8e637a2187 100644 --- a/Simulations/fd2/138/fd2138f941c9231f458679767081d36f8755fe7d/96cc0e7df5b0a0336bffb06345e68c98849772e8/README.yaml +++ b/Simulations/fd2/138/fd2138f941c9231f458679767081d36f8755fe7d/96cc0e7df5b0a0336bffb06345e68c98849772e8/README.yaml @@ -56,9 +56,14 @@ SOFTWARE: gromacs DIR_WRK: /media/osollila/Data/tmp/DATABANK/ ID: 377 bioschema_properties: - name: Molecular dynamics trajectory of a SOD/POPG/POPE/CLA (44:38:13:5) bilayer at 310 K (CHARMM36, GROMACS 5.1.2, 100 ns) [NMRlipids simulation 377] + name: Molecular dynamics trajectory of a SOD/POPG/POPE/CLA (44:38:13:5) bilayer + at 310 K (CHARMM36, GROMACS 5.1.2, 100 ns) [NMRlipids simulation 377] alternateName: 374POPG_126POPE_25000SOL_423SOD_49CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 423 SOD (44 mol%), 374 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 38 mol%), 126 POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 13 mol%) and 49 CLA (5 mol%) at 310 K. Simulated with CHARMM36 in GROMACS 5.1.2 for 100 ns (138720 atoms). Deposited as NMRlipids Databank simulation 377 and available from https://doi.org/10.5281/zenodo.2580153. + description: Molecular dynamics trajectory of a lipid bilayer of 423 SOD (44 mol%), + 374 POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 38 mol%), 126 POPE + (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 13 mol%) and 49 CLA (5 + mol%) at 310 K. Simulated with CHARMM36 in GROMACS 5.1.2 for 100 ns (138720 atoms). + Deposited as NMRlipids Databank simulation 377 and available from https://doi.org/10.5281/zenodo.2580153. sameAs: https://doi.org/10.5281/zenodo.2580153 datePublished: '2019-02-28' license: @@ -151,7 +156,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.2580153 identifier: 10.5281/zenodo.2580153 url: https://doi.org/10.5281/zenodo.2580153 - name: CHARMM36 POPG-POPE 3:1 Bilayer Simulation (Last 100 ns, 150 mM NaCl, 310 K ) + name: CHARMM36 POPG-POPE 3:1 Bilayer Simulation (Last 100 ns, 150 mM NaCl, 310 + K ) publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/fd8/18f/fd818f1fa1b32dcd80ac3a124e76bd2d73705abe/fd9cef87eca7bfbaac8581358f2d8f13d8d43cd1/README.yaml b/Simulations/fd8/18f/fd818f1fa1b32dcd80ac3a124e76bd2d73705abe/fd9cef87eca7bfbaac8581358f2d8f13d8d43cd1/README.yaml index 851baaca09..3f8016bf9d 100644 --- a/Simulations/fd8/18f/fd818f1fa1b32dcd80ac3a124e76bd2d73705abe/fd9cef87eca7bfbaac8581358f2d8f13d8d43cd1/README.yaml +++ b/Simulations/fd8/18f/fd818f1fa1b32dcd80ac3a124e76bd2d73705abe/fd9cef87eca7bfbaac8581358f2d8f13d8d43cd1/README.yaml @@ -55,9 +55,13 @@ EXPERIMENT: - 10.1021/acs.jctc.3c00648/9 ID: 91 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CHOL (53:47) bilayer at 298.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 91] + name: Molecular dynamics trajectory of a POPC/CHOL (53:47) bilayer at 298.15 K (CHARMM36, + GROMACS, 1001 ns) [NMRlipids simulation 91] alternateName: 64POPC_56CHOL_6000SOL_298K - description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 53 mol%) and 56 CHOL (cholesterol, 47 mol%) at 298.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (30720 atoms). Deposited as NMRlipids Databank simulation 91 and available from https://doi.org/10.5281/zenodo.5767451. + description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 53 mol%) and 56 CHOL (cholesterol, 47 mol%) at 298.15 K. Simulated with CHARMM36 + in GROMACS for 1001 ns (30720 atoms). Deposited as NMRlipids Databank simulation + 91 and available from https://doi.org/10.5281/zenodo.5767451. sameAs: https://doi.org/10.5281/zenodo.5767451 datePublished: '2021-12-08' license: diff --git a/Simulations/fde/619/fde619e4b59f665c97eafb23d201d793eb215117/9a28d5c7bb181fcc608f14343e483134a84a570f/README.yaml b/Simulations/fde/619/fde619e4b59f665c97eafb23d201d793eb215117/9a28d5c7bb181fcc608f14343e483134a84a570f/README.yaml index fdcb37cc76..dd87214696 100644 --- a/Simulations/fde/619/fde619e4b59f665c97eafb23d201d793eb215117/9a28d5c7bb181fcc608f14343e483134a84a570f/README.yaml +++ b/Simulations/fde/619/fde619e4b59f665c97eafb23d201d793eb215117/9a28d5c7bb181fcc608f14343e483134a84a570f/README.yaml @@ -44,9 +44,12 @@ EXPERIMENT: FORMFACTOR: [] ID: 578 bioschema_properties: - name: Molecular dynamics trajectory of a DOPC bilayer at 333.15 K (CHARMM36, GROMACS, 1001 ns) [NMRlipids simulation 578] + name: Molecular dynamics trajectory of a DOPC bilayer at 333.15 K (CHARMM36, GROMACS, + 1001 ns) [NMRlipids simulation 578] alternateName: 256DOPC_12800SOL_333K - description: Molecular dynamics trajectory of a lipid bilayer of 256 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (73728 atoms). Deposited as NMRlipids Databank simulation 578 and available from https://doi.org/10.5281/zenodo.6943413. + description: Molecular dynamics trajectory of a lipid bilayer of 256 DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) + at 333.15 K. Simulated with CHARMM36 in GROMACS for 1001 ns (73728 atoms). Deposited + as NMRlipids Databank simulation 578 and available from https://doi.org/10.5281/zenodo.6943413. sameAs: https://doi.org/10.5281/zenodo.6943413 datePublished: '2022-07-30' license: @@ -134,7 +137,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.6943413 identifier: 10.5281/zenodo.6943413 url: https://doi.org/10.5281/zenodo.6943413 - name: Simulations of different single-component bilayers, three different system sizes + name: Simulations of different single-component bilayers, three different system + sizes publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/fe7/a5a/fe7a5ae801fa82b7f8f336676835231d8c6b999f/31274d02ccdbbad2dd4b397cb760ce99c7c09e0f/README.yaml b/Simulations/fe7/a5a/fe7a5ae801fa82b7f8f336676835231d8c6b999f/31274d02ccdbbad2dd4b397cb760ce99c7c09e0f/README.yaml index db0f738ad0..258f0ac110 100644 --- a/Simulations/fe7/a5a/fe7a5ae801fa82b7f8f336676835231d8c6b999f/31274d02ccdbbad2dd4b397cb760ce99c7c09e0f/README.yaml +++ b/Simulations/fe7/a5a/fe7a5ae801fa82b7f8f336676835231d8c6b999f/31274d02ccdbbad2dd4b397cb760ce99c7c09e0f/README.yaml @@ -44,9 +44,13 @@ SOFTWARE: gromacs DIR_WRK: /usr/home/bort/Databank ID: 445 bioschema_properties: - name: Molecular dynamics trajectory of a DOPS/SOD (50:50) bilayer at 303 K (Slipids, GROMACS, 100 ns) [NMRlipids simulation 445] + name: Molecular dynamics trajectory of a DOPS/SOD (50:50) bilayer at 303 K (Slipids, + GROMACS, 100 ns) [NMRlipids simulation 445] alternateName: 128DOPS_4880SOL_128SOD_303K_v2 - description: Molecular dynamics trajectory of a lipid bilayer of 128 DOPS (1,2-dioleoyl-sn-glycero-3-phospho-L-serine, 50 mol%) and 128 SOD (50 mol%) at 303 K. Simulated with Slipids in GROMACS for 100 ns (30336 atoms). Deposited as NMRlipids Databank simulation 445 and available from https://doi.org/10.5281/zenodo.1129439. + description: Molecular dynamics trajectory of a lipid bilayer of 128 DOPS (1,2-dioleoyl-sn-glycero-3-phospho-L-serine, + 50 mol%) and 128 SOD (50 mol%) at 303 K. Simulated with Slipids in GROMACS for + 100 ns (30336 atoms). Deposited as NMRlipids Databank simulation 445 and available + from https://doi.org/10.5281/zenodo.1129439. sameAs: https://doi.org/10.5281/zenodo.1129439 datePublished: '2017-12-24' license: diff --git a/Simulations/ff9/319/ff931999796a0eb1f6d9a8f1b31bf0fe234693a6/9aec00428151f523210240dc99bfa4cde60e37e9/README.yaml b/Simulations/ff9/319/ff931999796a0eb1f6d9a8f1b31bf0fe234693a6/9aec00428151f523210240dc99bfa4cde60e37e9/README.yaml index f0d67a9d04..5aa32485c2 100644 --- a/Simulations/ff9/319/ff931999796a0eb1f6d9a8f1b31bf0fe234693a6/9aec00428151f523210240dc99bfa4cde60e37e9/README.yaml +++ b/Simulations/ff9/319/ff931999796a0eb1f6d9a8f1b31bf0fe234693a6/9aec00428151f523210240dc99bfa4cde60e37e9/README.yaml @@ -49,9 +49,14 @@ SOFTWARE: gromacs DIR_WRK: /usr/home/bort/Databank ID: 297 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/SOD (67:16:16) bilayer at 310 K (Slipids for lipids, Kohagen for NaCl, GROMACS 4.6, 100 ns) [NMRlipids simulation 297] + name: Molecular dynamics trajectory of a POPC/CLA/SOD (67:16:16) bilayer at 310 + K (Slipids for lipids, Kohagen for NaCl, GROMACS 4.6, 100 ns) [NMRlipids simulation + 297] alternateName: 200POPC_9000SOL_49SOD_49CLA_310K - description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 67 mol%), 49 CLA (16 mol%) and 49 SOD (16 mol%) at 310 K. Simulated with Slipids for lipids, Kohagen for NaCl in GROMACS 4.6 for 100 ns (53898 atoms). Deposited as NMRlipids Databank simulation 297 and available from https://doi.org/10.5281/zenodo.35193. + description: Molecular dynamics trajectory of a lipid bilayer of 200 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 67 mol%), 49 CLA (16 mol%) and 49 SOD (16 mol%) at 310 K. Simulated with Slipids + for lipids, Kohagen for NaCl in GROMACS 4.6 for 100 ns (53898 atoms). Deposited + as NMRlipids Databank simulation 297 and available from https://doi.org/10.5281/zenodo.35193. sameAs: https://doi.org/10.5281/zenodo.35193 datePublished: '2015-12-11' license: diff --git a/Simulations/ffa/c21/ffac217b6e195c9b67d38b35463276971eecf411/db247acb1f0ff10480672de8c570de3944ab87d2/README.yaml b/Simulations/ffa/c21/ffac217b6e195c9b67d38b35463276971eecf411/db247acb1f0ff10480672de8c570de3944ab87d2/README.yaml index 144707d166..0cdfa507d4 100644 --- a/Simulations/ffa/c21/ffac217b6e195c9b67d38b35463276971eecf411/db247acb1f0ff10480672de8c570de3944ab87d2/README.yaml +++ b/Simulations/ffa/c21/ffac217b6e195c9b67d38b35463276971eecf411/db247acb1f0ff10480672de8c570de3944ab87d2/README.yaml @@ -62,9 +62,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 48 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/CLA/CAL/POPS/SOD (37:32:16:7:7) bilayer at 298 K (Lipid17 and Dang ions, GROMACS 2018.0, 975 ns) [NMRlipids simulation 48] + name: Molecular dynamics trajectory of a POPC/CLA/CAL/POPS/SOD (37:32:16:7:7) bilayer + at 298 K (Lipid17 and Dang ions, GROMACS 2018.0, 975 ns) [NMRlipids simulation + 48] alternateName: 60POPC_12POPS_3522SOL_26CAL_52CLA_12SOD_298K - description: Molecular dynamics trajectory of a lipid bilayer of 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 37 mol%), 52 CLA (32 mol%), 26 CAL (16 mol%), 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 7 mol%) and 12 SOD (7 mol%) at 298 K. Simulated with Lipid17 and Dang ions in GROMACS 2018.0 for 975 ns (20220 atoms). Deposited as NMRlipids Databank simulation 48 and available from https://doi.org/10.5281/zenodo.1487761. + description: Molecular dynamics trajectory of a lipid bilayer of 60 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 37 mol%), 52 CLA (32 mol%), 26 CAL (16 mol%), 12 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, + 7 mol%) and 12 SOD (7 mol%) at 298 K. Simulated with Lipid17 and Dang ions in + GROMACS 2018.0 for 975 ns (20220 atoms). Deposited as NMRlipids Databank simulation + 48 and available from https://doi.org/10.5281/zenodo.1487761. sameAs: https://doi.org/10.5281/zenodo.1487761 datePublished: '2018-11-14' license: @@ -156,7 +162,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1487761 identifier: 10.5281/zenodo.1487761 url: https://doi.org/10.5281/zenodo.1487761 - name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS with the lipid17 force field, only counterions, and CaCl2 concentrations + name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS + with the lipid17 force field, only counterions, and CaCl2 concentrations publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/ffc/695/ffc695f5b69834f1f2a20d611df200be75eeaa00/20ff24d8995731f57335165c47a58c75b0b5ea26/README.yaml b/Simulations/ffc/695/ffc695f5b69834f1f2a20d611df200be75eeaa00/20ff24d8995731f57335165c47a58c75b0b5ea26/README.yaml index f09a0e768d..9d6e45230a 100644 --- a/Simulations/ffc/695/ffc695f5b69834f1f2a20d611df200be75eeaa00/20ff24d8995731f57335165c47a58c75b0b5ea26/README.yaml +++ b/Simulations/ffc/695/ffc695f5b69834f1f2a20d611df200be75eeaa00/20ff24d8995731f57335165c47a58c75b0b5ea26/README.yaml @@ -55,9 +55,15 @@ EXPERIMENT: FORMFACTOR: [] ID: 380 bioschema_properties: - name: Molecular dynamics trajectory of a POPC/POPS/SOD (33:33:33) bilayer at 298 K (ECC-lipids, SPCE water model, ECC-ions, GROMACS 2018.0, 1000 ns) [NMRlipids simulation 380] + name: Molecular dynamics trajectory of a POPC/POPS/SOD (33:33:33) bilayer at 298 + K (ECC-lipids, SPCE water model, ECC-ions, GROMACS 2018.0, 1000 ns) [NMRlipids + simulation 380] alternateName: 64POPS_64POPC_5253SOL_64SOD_298K_ECC-lipid - description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 33 mol%), 64 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 33 mol%) and 64 SOD (33 mol%) at 298 K. Simulated with ECC-lipids, SPCE water model, ECC-ions in GROMACS 2018.0 for 1000 ns (32527 atoms). Deposited as NMRlipids Databank simulation 380 and available from https://doi.org/10.5281/zenodo.1488094. + description: Molecular dynamics trajectory of a lipid bilayer of 64 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, + 33 mol%), 64 POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine, 33 mol%) + and 64 SOD (33 mol%) at 298 K. Simulated with ECC-lipids, SPCE water model, ECC-ions + in GROMACS 2018.0 for 1000 ns (32527 atoms). Deposited as NMRlipids Databank simulation + 380 and available from https://doi.org/10.5281/zenodo.1488094. sameAs: https://doi.org/10.5281/zenodo.1488094 datePublished: '2018-11-14' license: @@ -148,7 +154,8 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.1488094 identifier: 10.5281/zenodo.1488094 url: https://doi.org/10.5281/zenodo.1488094 - name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS (various mixtures) with ECC-lipids force field, and Na+ (K+) counterions + name: Molecular dynamics simulations of lipid bilayers containing POPC and POPS + (various mixtures) with ECC-lipids force field, and Na+ (K+) counterions publisher: Zenodo accessRights: openAccess _source: diff --git a/Simulations/ffd/1b3/ffd1b3aeaa35e0243d247c80ec8ef931201b19f5/ffd1b3aeaa35e0243d247c80ec8ef931201b19f5/README.yaml b/Simulations/ffd/1b3/ffd1b3aeaa35e0243d247c80ec8ef931201b19f5/ffd1b3aeaa35e0243d247c80ec8ef931201b19f5/README.yaml index 9dcb2fa393..0f16e3d7cd 100644 --- a/Simulations/ffd/1b3/ffd1b3aeaa35e0243d247c80ec8ef931201b19f5/ffd1b3aeaa35e0243d247c80ec8ef931201b19f5/README.yaml +++ b/Simulations/ffd/1b3/ffd1b3aeaa35e0243d247c80ec8ef931201b19f5/ffd1b3aeaa35e0243d247c80ec8ef931201b19f5/README.yaml @@ -37,9 +37,13 @@ EXPERIMENT: - 10.1021/bi00218a003/2 FORMFACTOR: [] bioschema_properties: - name: Molecular dynamics trajectory of a PILPC bilayer at 303.15 K (CHARMM36m, NAMD 3.0, 500 ns) [NMRlipids simulation 906] + name: Molecular dynamics trajectory of a PILPC bilayer at 303.15 K (CHARMM36m, NAMD + 3.0, 500 ns) [NMRlipids simulation 906] alternateName: PiLPC - description: Molecular dynamics trajectory of a lipid bilayer of 200 PILPC (1-Palmitoyl-2-isolinoleoyl phosphatidylcholine) at 303.15 K. Simulated with CHARMM36m in NAMD 3.0 for 500 ns (51600 atoms). Deposited as NMRlipids Databank simulation 906 and available from https://doi.org/10.5281/zenodo.18480411. + description: Molecular dynamics trajectory of a lipid bilayer of 200 PILPC (1-Palmitoyl-2-isolinoleoyl + phosphatidylcholine) at 303.15 K. Simulated with CHARMM36m in NAMD 3.0 for 500 + ns (51600 atoms). Deposited as NMRlipids Databank simulation 906 and available + from https://doi.org/10.5281/zenodo.18480411. sameAs: https://doi.org/10.5281/zenodo.18480411 datePublished: '2026-02-04' license: @@ -130,7 +134,9 @@ bioschema_properties: '@id': https://doi.org/10.5281/zenodo.18480411 identifier: 10.5281/zenodo.18480411 url: https://doi.org/10.5281/zenodo.18480411 - name: PLPC (PiLPC) lipid bilayer | 1-palmitoyl-2-isolinoleoyl-i«-glycero-3-phosphocholine with C6-C7 and the C9-C10 double bonds | 303K, CHARMM36m-WYF forcefield, NAMD 3.0.2, 2* 500 ns + name: PLPC (PiLPC) lipid bilayer | 1-palmitoyl-2-isolinoleoyl-i«-glycero-3-phosphocholine + with C6-C7 and the C9-C10 double bonds | 303K, CHARMM36m-WYF forcefield, NAMD + 3.0.2, 2* 500 ns publisher: Zenodo _source: api: datacite