Guidance for building, checking, debugging, and automating GROMACS molecular simulations. GROMACS is software that models how molecules move over time.

Use it for preprocessing, topology and coordinate files, simulation parameters, energy minimization, equilibration, production runs, analysis, restarts, and scheduled cluster jobs.

It organizes the many stages and input files involved in a simulation, helping prevent incompatible parameters, incomplete restarts, and cluster-launch errors.

hpc-gromacs — Skill for Codex by SciMate-AI

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent

npx skills add SciMate-AI/HPC-Skills --skill hpc-gromacs

Clone the repo

git clone --depth 1 https://github.com/SciMate-AI/HPC-Skills

Made for: Codex.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

README.md

[![agentmods](https://agentmods.dev/badge/skills/scimate-ai/hpc-skills/hpc-gromacs/github.svg)](https://agentmods.dev/skills/scimate-ai/hpc-skills/hpc-gromacs)

Your own site

<a href="https://agentmods.dev/skills/scimate-ai/hpc-skills/hpc-gromacs"><img src="https://agentmods.dev/badge/skills/scimate-ai/hpc-skills/hpc-gromacs/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

Your own site · 80×15

<a href="https://agentmods.dev/skills/scimate-ai/hpc-skills/hpc-gromacs"><img src="https://agentmods.dev/badge/skills/scimate-ai/hpc-skills/hpc-gromacs.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 61 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 513 The whole file, excluding the scripts and references it only reads on demand.

Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.

Origin original No closer match found in the catalogue.

Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

Model	Per session	Once invoked
Fable 5.1	$0.00061	$0.00513
Opus 5	$0.00030	$0.00257
Sonnet 5	$0.00012	$0.00103
Haiku 4.5	$0.00006	$0.00051

Measured 12d ago against content hash fa04ffb71333, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-11, from the pricing page.

Security

Grade A, and why

hpc-gromacs scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 12d ago.

The scan reads SKILL.md. This mod also ships 1 executable file (assets/templates/gromacs-mdrun-slurm.sh), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

skills/hpc-gromacs/SKILL.md · 52 lines

What it actually says

HPC GROMACS

Treat GROMACS as a staged workflow from preprocessing to analysis.

Start

Read references/workflow-manual.md before building a run pipeline.
Read references/file-and-parameter-matrix.md when mapping .mdp, topology, structure, and index responsibilities.
Read references/ensembles-and-analysis.md when choosing minimization, NVT, NPT, production, and standard analysis commands.
Read references/cluster-execution-playbook.md when staging a GROMACS workflow for scheduler-backed cluster execution.
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

Files

What ships with it

14 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

12d ago First seen · 52 lines · 61 tokens per session scan A fa04ffb71333

Subscribe to this mod's changes

hpc-gromacs is a skill published in the GitHub repository SciMate-AI/HPC-Skills (86 stars, last pushed 5mo ago), licensed MIT. It adds 61 tokens to every session and 513 once invoked, about $0.0003 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

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