Deprecate the GROMACS patch

[njzjz]

The GROMACS patch in the deepmd-kit repository has not been updated for 5 years, and it seems no one is familiar with it or willing to contribute. Thus, we decide to deprecate it. Documentation will be updated soon.

Note: there is a third-party version at https://arxiv.org/abs/2602.02234, which was claimed to be better.

[njzjz-bot]

Planned implementation for this issue:

1. Remove the in-tree GROMACS integration completely

• delete source/gmx/
• remove the GROMACS-specific CMake target / variables / subdirectory wiring from source/CMakeLists.txt
• remove any packaging / install references that were only needed for the old patch flow

2. Replace the old GROMACS documentation with deprecation notices

• replace doc/install/install-gromacs.md with a deprecation notice similar to doc/install/build-conda.md
• replace doc/third-party/gromacs.md with a deprecation notice as well
• the notice will explicitly say that the official GROMACS patch shipped in this repository is no longer maintained and has been removed/deprecated
• the notice will also point users to maintained alternatives:
  • the official LAMMPS interface in DeePMD-kit for supported production use
  • the third-party GROMACS implementation mentioned in the issue note

3. Clean up cross-references after removal

• update install / third-party indices so they no longer present the removed GROMACS path as a supported in-tree integration
• update files such as README.md, AGENTS.md, troubleshooting / install docs, and any other references that still describe source/gmx, the GROMACS plugin, or the patch workflow as part of the repository
• remove or adjust example/documentation references that become orphaned after the removal

4. Sanity check

• run a repository-wide grep afterwards to make sure no stale in-tree build instructions remain for the removed GROMACS patch, except for the new deprecation notices and external alternative references

If this scope looks good, I will send a PR implementing exactly the above.

— OpenClaw 2026.3.28 (model: gpt-5.4)