Astropy
zLanqing/codex-claude-academic-skills
Comprehensive Python library for astronomy and astrophysics.
Prepare, validate, run, resume, troubleshoot, and analyze GROMACS molecular dynamics.
Install Gromacs
$ npx skills add JCLiuGroup/AI-Computational-Chemist --skill gromacs -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install JCLiuGroup/AI-Computational-Chemist gromacs --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/JCLiuGroup/AI-Computational-Chemist.git skills-src && mkdir -p .claude/skills && cp -r skills-src/tools/gromacs .claude/skills/gromacs && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "gromacs" agent skill from https://github.com/JCLiuGroup/AI-Computational-Chemist/tree/main/tools/gromacs into .claude/skills/gromacs/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gromacs", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/JCLiuGroup/AI-Computational-Chemist/tree/main/tools/gromacsType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add JCLiuGroup/AI-Computational-Chemist --skill gromacs -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install JCLiuGroup/AI-Computational-Chemist gromacs --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/JCLiuGroup/AI-Computational-Chemist.git skills-src && mkdir -p .agents/skills && cp -r skills-src/tools/gromacs .agents/skills/gromacs && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "gromacs" agent skill from https://github.com/JCLiuGroup/AI-Computational-Chemist/tree/main/tools/gromacs into .agents/skills/gromacs/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gromacs", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add JCLiuGroup/AI-Computational-Chemist --skill gromacs -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install JCLiuGroup/AI-Computational-Chemist gromacs --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/JCLiuGroup/AI-Computational-Chemist.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/tools/gromacs .cursor/skills/gromacs && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "gromacs" agent skill from https://github.com/JCLiuGroup/AI-Computational-Chemist/tree/main/tools/gromacs into .cursor/skills/gromacs/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gromacs", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/JCLiuGroup/AI-Computational-Chemist.git --path tools/gromacs--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add JCLiuGroup/AI-Computational-Chemist --skill gromacs -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install JCLiuGroup/AI-Computational-Chemist gromacs --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/JCLiuGroup/AI-Computational-Chemist.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/tools/gromacs .gemini/skills/gromacs && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "gromacs" agent skill from https://github.com/JCLiuGroup/AI-Computational-Chemist/tree/main/tools/gromacs into .gemini/skills/gromacs/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gromacs", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install JCLiuGroup/AI-Computational-Chemist gromacsInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add JCLiuGroup/AI-Computational-Chemist --skill gromacs -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/JCLiuGroup/AI-Computational-Chemist.git skills-src && mkdir -p .github/skills && cp -r skills-src/tools/gromacs .github/skills/gromacs && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "gromacs" agent skill from https://github.com/JCLiuGroup/AI-Computational-Chemist/tree/main/tools/gromacs into .github/skills/gromacs/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gromacs", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add JCLiuGroup/AI-Computational-Chemist --skill gromacs -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install JCLiuGroup/AI-Computational-Chemist gromacs --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/JCLiuGroup/AI-Computational-Chemist.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/tools/gromacs .opencode/skills/gromacs && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "gromacs" agent skill from https://github.com/JCLiuGroup/AI-Computational-Chemist/tree/main/tools/gromacs into .opencode/skills/gromacs/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gromacs", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
gromacs- GitHub stars
- 146
- Used in
- 1 other repo
- Token cost
- ~1.7k tokens
- SKILL.md length
- 724 words
- Files
- 17 (incl. scripts, references)
- Skills in repo
- 21
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
Prepare, validate, run, resume, troubleshoot, and analyze GROMACS molecular dynamics.
- Works in 10 steps: Inspect the structure before converting.… → Choose one coherent parameter family.… → Build the system. Generate topology,… → …
- Biomolecular and molecular-condensed-phase classical MD
- SKILL.md covers Required inputs, Where to find what, Workflow and Hard guardrails
- Runs Python scripts from its folder; calls python
What it does
Gromacs is an agent skill from JCLiuGroup/AI-Computational-Chemist. Prepare, validate, run, resume, troubleshoot, and analyze GROMACS molecular dynamics. Use for biomolecular and molecular-condensed-phase classical MD; PDB/GRO/ITP/TOP/MDP/TPR workflows; force-field/topology integration; EM/NVT/NPT/production; checkpoint continuation; PBC repair; RMSD/RMSF/RDF/MSD/SASA/hydrogen-bond/density/membrane analysis; and VMD handoff.
Its SKILL.md is about 1.7k tokens, which your agent loads only when the skill is triggered. The skill folder holds 19 other files, including scripts and reference files (for example `examples/README.md`, `references/analysis.md` and `references/biomolecules.md`).
It sits in Research & Science, covering Physical and earth sciences.
When your agent uses it
- Biomolecular and molecular-condensed-phase classical MD
- PDB/GRO/ITP/TOP/MDP/TPR workflows
- Force-field/topology integration
- EM/NVT/NPT/production
Example prompts
- “/gromacs”
Requirements
- Python 3
Workflow steps
10 steps, taken from the first numbered list in SKILL.md.
- Inspect the structure before converting. Resolve alternate locations/models, missing atoms/residues, protonation, termini, special bonds…
- Choose one coherent parameter family. Record force field, water/ion model, ligand parameter source, charge method and every compatibility…
- Build the system. Generate topology, define the box, add solvent/ions/other components, and make coordinate order match [ molecules ]…
- Static preflight. Run the checker; then run gmx grompp -pp processed.top -po mdout.mdp and inspect warnings, processed topology and actual…
- Energy minimize. Validate finite energy, convergence criterion and absence of severe clashes.
- Equilibrate in explicit stages. Stabilize temperature, then pressure/density/box as required, with restraints reduced according to a…
- Production. Continue from checkpoint/state, do not regenerate velocities, and preserve raw outputs.
- Validate technically and scientifically. A clean mdrun is not evidence of equilibration or adequate sampling.
- Derive analysis-specific trajectories. Keep the raw trajectory immutable; make separate whole/centered/fitted/unwrapped copies for…
- Report provenance: force field, water/ions, topology sources, GROMACS version, full .mdp, equilibration cut, production interval…
What it can do on your machine
Read from SKILL.md and the folder at commit e27b555. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Ships 2 files in scripts/ (Python), which the agent can run.
Shell commands in SKILL.md call:
python
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Gromacs loads about 1.7k tokens when it runs, and up to ~17k if it reads all its reference files. Until then it costs about 92 tokens; SKILL.md has 724 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check passed
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.
SKILL.md
Its licence (Custom licence) doesn't allow us to republish the file, so here is its outline and opening line. It has 724 words (~1,711 tokens).
“GROMACS owns the code-specific path for classical molecular dynamics: build a chemically and topologically consistent system, compile each stage with gmx grompp, run with gmx mdrun, validate every stage, and analyze only verified production segments. Tool-agnostic force-field and sampling science…”
- name
- gromacs
Files
SKILL.md and 16 other files (scripts, references) in tools/gromacs of JCLiuGroup/AI-Computational-Chemist.
- SKILL.md
- examples/README.md
- references/analysis.md
- references/biomolecules.md
- references/errors.md
- references/ligands-small-molecules.md
- references/liquids-interfaces.md
- references/mdp-options.md
- references/membranes.md
- references/resources.md
- references/running.md
- references/system-preparation.md
- references/topology-and-force-fields.md
- references/validation.md
- references/vmd-handoff.md
- scripts/check_gromacs_inputs.py
- scripts/parse_gromacs_log.py
Open the folder on GitHubat commit e27b555
Used in 1 other repository
We found 2 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in JCLiuGroup/AI-Computational-Chemist, which our catalogue first saw on October 7, 2026.
Compare with similar skills
Gromacs next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Gromacs this skillJCLiuGroup/AI-Computational-Chemist | 146 | 1 repos | ~1.7k | Automated safety check: Pass | Custom licence | |
| AstropyzLanqing/codex-claude-academic-skills | 4.7k | 13 repos | ~2.9k | Automated safety check: Pass | BSD-3-Clause | |
| PymatgenzLanqing/codex-claude-academic-skills | 4.7k | 11 repos | ~5k | Automated safety check: Pass | MIT | |
| Cantera Ignition DelayK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~2.2k | Automated safety check: Pass | MIT | |
| Weathertrpc-group/trpc-agent-go | 1.9k | 8 repos | ~591 | Automated safety check: Pass | Apache-2.0 | |
| Pymol VisualizationChatMol/ChatMol | 373 | — | ~1.2k | Automated safety check: Pass | MIT |
Similar skills
Pymatgen
zLanqing/codex-claude-academic-skills
Materials science toolkit. An agent skill from zLanqing/codex-claude-academic-skills.
Cantera Ignition Delay
K-Dense-AI/scientific-agent-skills
Runs Cantera constant-volume or constant-pressure ignition simulations and reports temperature-based ignition delay with mechanism provenance and checks.
Weather
trpc-group/trpc-agent-go
Get current weather and forecasts via wttr.in or Open-Meteo.
Pymol Visualization
ChatMol/ChatMol
Generate publication-quality molecular visualization images using PyMOL.
Review
Muuuun/luxas
Write domain-authentic review articles that synthesize rather than stack.
More from JCLiuGroup/AI-Computational-Chemist
All 21 skills in this repoResearch Orchestrator
JCLiuGroup/AI-Computational-Chemist
Define and maintain machine-readable research project state for multi-stage computational chemistry work.
Comp Chem Workflow
JCLiuGroup/AI-Computational-Chemist
Entry point and controller for computational chemistry and materials workflows.
Cp2k
JCLiuGroup/AI-Computational-Chemist
Prepare, validate, run, and troubleshoot CP2K calculations for periodic and large molecular systems.
Deepmd
JCLiuGroup/AI-Computational-Chemist
DeePMD-kit and Deep Potential Molecular Dynamics workflows. An agent skill from JCLiuGroup/AI-Computational-Chemist.
Gaussian
JCLiuGroup/AI-Computational-Chemist
Prepare, validate, and troubleshoot Gaussian molecular quantum chemistry jobs.
Hpc Submit
JCLiuGroup/AI-Computational-Chemist
Submit, monitor, and recover computational chemistry jobs locally, over approved SSH targets, or through Slurm/PBS schedulers.
Related
Categories
Questions about Gromacs
What does Gromacs do?
Prepare, validate, run, resume, troubleshoot, and analyze GROMACS molecular dynamics. Gromacs is an agent skill from JCLiuGroup/AI-Computational-Chemist. Prepare, validate, run, resume, troubleshoot, and analyze GROMACS molecular dynamics.
When should I use Gromacs?
Gromacs fits situations like: biomolecular and molecular-condensed-phase classical MD; PDB/GRO/ITP/TOP/MDP/TPR workflows; force-field/topology integration; EM/NVT/NPT/production.
How do I install Gromacs in Claude Code?
Run `npx skills add JCLiuGroup/AI-Computational-Chemist --skill gromacs -a claude-code`. Or copy the skill folder (tools/gromacs in JCLiuGroup/AI-Computational-Chemist) into .claude/skills/gromacs in your project. Claude Code loads it when a task matches its description.
How do I install Gromacs in Codex?
Run `npx skills add JCLiuGroup/AI-Computational-Chemist --skill gromacs -a codex`. Or copy the skill folder (tools/gromacs in JCLiuGroup/AI-Computational-Chemist) into .agents/skills/gromacs in your project. Codex loads it when a task matches its description.
Can I use Gromacs in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add JCLiuGroup/AI-Computational-Chemist --skill gromacs -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/gromacs, .gemini/skills/gromacs, .github/skills/gromacs and .opencode/skills/gromacs in your project.
What does Gromacs need to run?
Going by SKILL.md and its folder, Gromacs needs Python for the scripts in its folder and the command-line tools its instructions call (python). Our summary lists: Python 3.
Does Gromacs access the network?
SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.
Is Gromacs safe to install?
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.
What licence does Gromacs use?
Gromacs has a licence file (the repository's licence) that doesn't match a standard licence. Read it on GitHub before reusing the skill.
How many tokens does Gromacs use?
About 1.7k tokens (SKILL.md is roughly 6.8k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 16k tokens, read only when the agent opens those files.
What are the alternatives to Gromacs?
Skills that share tags, products or a category with Gromacs: Astropy (zLanqing/codex-claude-academic-skills, 4.7k stars), Pymatgen (zLanqing/codex-claude-academic-skills, 4.7k stars), Cantera Ignition Delay (K-Dense-AI/scientific-agent-skills, 48k stars) and Weather (trpc-group/trpc-agent-go, 1.9k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Gromacs?
JCLiuGroup (a GitHub organization) maintains it in JCLiuGroup/AI-Computational-Chemist, which has 146 GitHub stars. The repository holds 21 skills in this directory. The repository was last updated on September 27, 2026.
Source: JCLiuGroup/AI-Computational-Chemist on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.