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Docs: what the GROMACS interfaces support, in the master manual #1507

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28 changes: 23 additions & 5 deletions new-manual/mdcodes.md
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Expand Up @@ -24,11 +24,29 @@ As far as we know, the following MD codes can be used with PLUMED out of the box
- [Metalwalls](https://gitlab.com/ampere2/metalwalls)
- [ASE](https://wiki.fysik.dtu.dk/ase/)
- [GPUMD](https://gpumd.org/)
- [GROMACS](https://www.gromacs.org/) as of version 2025, with limited support (no replica exchange, no [ENERGY](ENERGY.md) collective variable, no lambda dynamics).

We also provide patches for [namd](https://www.ks.uiuc.edu/Research/namd/) and [quantum espresso](https://www.quantum-espresso.org) as well as a
patch for [GROMACS](https://www.gromacs.org/) that you should use in place of the native implementation if you want to do replica exchange,
use the [ENERGY](ENERGY.md) collective variable or do lambda dynamics.
- [GROMACS](https://www.gromacs.org/) as of version 2025, with limited support (see the table below).

We also provide patches for [namd](https://www.ks.uiuc.edu/Research/namd/), [quantum espresso](https://www.quantum-espresso.org) and
[GROMACS](https://www.gromacs.org/) (`plumed patch --list-engines` lists them). The patches for GROMACS 2025 and 2026 add features to the
PLUMED interface that GROMACS includes since version 2025, and the patch for GROMACS 2024 has some more:

| 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](ENERGY.md) 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](COMMITTOR.md)) | 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 |

Notes on the table:

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](ENERGY.md), PLUMED updates (e.g. deposits its bias) with the energy before the shells are relaxed.

If you maintain another MD code that is PLUMED-ready let us know and we will add it to this list.

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