gromacs-md

GROMACS Molecular Dynamics

Use GROMACS for classical biomolecular MD workflows: protein or protein-ligand systems, membrane proteins, conformational dynamics, trajectory analysis, and approximate binding free energy post-processing.

This skill is intentionally lightweight. Use it to enforce the scientific workflow and risk checks; use local gmx, official GROMACS documentation, and optional scholaraio toolref for exact command syntax and version-specific .mdp details.

Local Environment

Prefer gmx on PATH. If GROMACS is installed elsewhere, set:

$env:GMX_EXE = "C:\path\to\gromacs\bin\gmx.exe"

Optional: set PYMOL_EXE for PyMOL rendering helpers in the companion skills.

The local scholaraio toolref GROMACS index contains the official current mdp-options source as version manual-current-mdp with 323 records. Full scholaraio toolref fetch gromacs may still require GitHub access; if it fails, the installed MDP index is enough for high-risk .mdp parameter lookup.

Verify before running real work:

gmx --version

For ligand and free-energy workflows, check optional tools before promising execution:

Get-Command acpype,antechamber,gmx_MMPBSA -ErrorAction SilentlyContinue

Protocol

Classify the user's request first:

1. gmx subcommand or command-line troubleshooting
2. .mdp parameter design or review
3. topology, force field, ligand, membrane, or box-building workflow
4. production execution and performance
5. trajectory analysis, visualization, or MM/PBSA-style post-processing

Before writing .mdp files, verify high-risk parameters: thermostat, barostat, constraints, cutoffs, PME, neighbor search, output frequency, coupling groups, timestep, and production ensemble.

If scholaraio is installed, use toolref-first:

scholaraio toolref search gromacs "temperature coupling"
scholaraio toolref show gromacs mdp integrator
scholaraio toolref show gromacs mdp pcoupl
scholaraio toolref show gromacs mdp tau-t
scholaraio toolref show gromacs mdp ref-t