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name: hpc-gromacs description: Build, review, debug, and automate GROMACS molecular simulation workflows. Use when working with GROMACS preprocessing, topology and coordinate files, .mdp parameters, energy minimization, equilibration, production MD, analysis commands, or GROMACS runtime errors.

HPC GROMACS

Treat GROMACS as a staged workflow from preprocessing to analysis.

Start

1. Read references/workflow-manual.md before building a run pipeline.
2. Read references/file-and-parameter-matrix.md when mapping .mdp, topology, structure, and index responsibilities.
3. Read references/ensembles-and-analysis.md when choosing minimization, NVT, NPT, production, and standard analysis commands.
4. Read references/cluster-execution-playbook.md when staging a GROMACS workflow for scheduler-backed cluster execution.
5. Read references/error-recovery.md when grompp, mdrun, or analysis commands fail.

Additional References

Load these on demand:

• references/topology-and-system-building.md for pdb2gmx, box setup, solvation, and ion insertion workflows
• references/restarts-and-output-control.md for checkpointing, append behavior, and long-job continuation
• references/mdp-coupling-and-constraints-matrix.md for thermostat, barostat, constraints, and timestep compatibility
• references/cluster-execution-playbook.md for grompp to mdrun staging, continuation, and cluster launch choices

Reusable Templates

Use assets/templates/ when a concrete starting scaffold is needed, especially:

• em.mdp
• nvt.mdp
• npt.mdp
• md_prod.mdp
• gromacs-mdrun-slurm.sh

Guardrails

• Do not skip grompp validation and jump straight into mdrun.
• Do not mix force fields, water models, and topology assumptions casually.
• Do not copy .mdp cutoffs, timesteps, or coupling settings without checking the intended force field and ensemble.
• Do not treat warnings from grompp as harmless by default.

Outputs

Summarize:

• input structure and topology sources
• .mdp stage and ensemble
• generated run artifact names such as .tpr
• analysis outputs requested or still needed