[invemichele-peptone]

Description

This PR was the port of #1505 and #1506 to master. These have now reached master with the merge of v2.10 (e879e3a): I checked that the 2024.3, 2025.0 and 2026.0 patches and the kernel fixes in master are the same as in v2.10, apart from PLUMED_LOG_FILE in the 2025 patch. Their follow-ups, #1508 (v2.9) and #1509 (v2.10), can reach master in the same way. A port here would only duplicate them, and conflict with the next merge.

So what is left is the part of the documentation that only master has: the table of what the GROMACS interfaces support, in new-manual/mdcodes.md. v2.10 has the same table in user-doc/Introduction.md (#1506, with the notes of #1509).

Feature	GROMACS 2025 or later, without patches	patches for GROMACS 2025 and 2026	patch for GROMACS 2024
biases on atoms, with domain decomposition and multiple time stepping	yes (1)	yes	yes
ENERGY collective variable and biases on the energy	no	yes (2,3)	yes (3)
multiple simulations that communicate through MPI (e.g. WALKERS_MPI)	no	yes	yes
PLUMED checkpoint data written at the steps of the GROMACS checkpoints	no	yes (2)	yes
PLUMED stopping the simulation (e.g. COMMITTOR)	no	yes	yes
polarizable models with shells	no	yes (4)	no
replica exchange with a PLUMED bias (-replex, -hrex)	no	no	yes
lambda dynamics (expanded ensemble)	no	no	yes

1. GROMACS 2026.0 to 2026.3 without patches stop at startup with more than one MPI rank.
2. Not with the modular simulator of GROMACS, the default for md-vv: set GMX_DISABLE_MODULAR_SIMULATOR=1.
3. With multiple time stepping, only on the steps when the slow forces are computed.
4. With ENERGY, PLUMED updates (e.g. deposits its bias) with the energy before the shells are relaxed.

The table replaces the sentence that suggested the patch for GROMACS 2025/2026 for replica exchange and lambda dynamics, which only the patch for GROMACS 2024 has. The cells follow the regression tests proposed to the PLUMED testcenter in plumed-testcenter/plumed-testcenter#95.

The CHANGES entries that came from v2.9 and v2.10 use \ref, which the master manual shows verbatim. I left them as they are: converting them here would conflict with the next merges of v2.10. The same holds for older entries.

Target release

I would like my code to appear in release v2.11

Type of contribution

• changes to code or doc authored by PLUMED developers, or additions of code in the core or within the default modules
• changes to a module not authored by you
• new module contribution or edit of a module authored by you

Copyright

• I agree to transfer the copyright of the code I have written to the PLUMED developers or to the author of the code I am modifying.
• the module I added or modified contains a COPYRIGHT file with the correct license information. Code should be released under an open source license. I also used the command cd src && ./header.sh mymodulename in order to make sure the headers of the module are correct.

Tests

• I added a new regtest or modified an existing regtest to validate my changes.
• I verified that all regtests are passed successfully on GitHub Actions.

🤖 Generated with Claude Code

[carlocamilloni]

@invemichele-peptone I am removing gromacs 2022 and 2023 patches from master, could you please update this to remove them here as well?

[invemichele]

ok, I'll tell Claude about it :)

[invemichele-peptone]

@carlocamilloni done: rebased on 6f73c1b, with the parts for GROMACS 2022 and 2023 dropped from all commits and the docs table now saying "patch for GROMACS 2024". Since #1505 and #1506 were merged while I was still running a last review, this also includes the fixes I found then, which are in two small follow-ups: #1508 (v2.9) and #1509 (v2.10). The description is updated.

🤖 Generated with Claude Code

[invemichele-peptone]

@carlocamilloni I see that you merged v2.10 into master, which brought #1505 and #1506 here: I checked that the GROMACS patches and the kernel fixes in master are now the same as in v2.10. So I reduced this PR to the only part that cannot come from v2.10: the table of the GROMACS interfaces in the master manual. The follow-ups #1508 and #1509 can reach master with the next merge of v2.10, without conflicts.

🤖 Generated with Claude Code