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Hpc Gromacs

skill-scimate-ai-hpc-skills-hpc-gromacs · by SciMate-AI

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.

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Install

$ agentstack add skill-scimate-ai-hpc-skills-hpc-gromacs

✓ scanned · ✓ verified — works with Claude Code, Cursor, and more.

Security review

✓ Passed

No issues found. Passed automated security review. · v0.1.0 How review works →

  • ✓ Prompt-injection patterns
  • ✓ Secret / credential exfiltration
  • ✓ Dangerous shell & filesystem operations
  • ✓ Untrusted network calls
  • ✓ Known-malicious package signatures

What it can access

  • ✓ Network access No
  • ✓ Filesystem access No
  • ✓ Shell / process execution No
  • ✓ Environment & secrets No
  • ✓ Dynamic code execution No

From automated source analysis of v0.1.0. “Used” means the capability is present in the source — more access means more to trust, not that it’s unsafe.

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About

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

Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

Install and usage instructions live in the source repository linked above.

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Versions

  • v0.1.0 Imported from the upstream source.

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