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Run npx skillmds@latest add huc-he/gromacs-md in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

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Which AI agents work with Gromacs Md?

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Is Gromacs Md free to use?

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Who published Gromacs Md?

HUC-he (@huc-he) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Gromacs Md by huc-he — Agent Skill

Name: Gromacs Md
Author: HUC-he

Gromacs Md

Automate GROMACS molecular dynamics (MD) simulations end-to-end. Use when the user wants to set up, run, debug, or analyze MD simulations with GROMACS/gmx, including protein, protein-ligand, peptide, nucleic-acid, or membrane systems; build topologies and .mdp files; run pdb2gmx, solvate, genion, grompp, mdrun; perform energy minimization, NVT/NPT equilibration, and production runs with GPU acceleration; analyze trajectories (RMSD, RMSF, Rg, hydrogen bonds, contacts, free energy); or troubleshoot GROMACS errors. Also triggered by Chinese requests containing GROMACS, gmx, or 分子动力学模拟, and Japanese requests containing 分子動力学シミュレーション.

HUC-he Updated Sep 22, 2026

File contents

GROMACS MD Automation

Goal

Take a user's system description and structure, then run a scientifically sound GROMACS MD simulation with minimal back-and-forth and report the results.

Language

Users may write in Chinese (中文), English, or Japanese (日本語). Respond in the language the user uses.

Workflow

0. Collect inputs (ask only for what is missing)

System type: protein / protein-ligand / nucleic acid / membrane / other
Structure: PDB ID, PDB file, or ligand SMILES/SDF (sequence-only -> suggest AlphaFold modeling first)
Goal: stability, conformational change, binding, free energy, etc.
Optional preferences: force field, water model, temperature (default 310 K), simulation length (default 100 ns), salt concentration

See references/workflow.md for the input table and default choices. Do not block on optional preferences; use the defaults.

1. Verify environment

Run:

gmx --version (expect GPU support: CUDA and GROMACS >= 2024)
nvidia-smi (GPU visible)

If missing or broken, fix the environment first (references/workflow.md, Environment section).

2. Create the project directory

Create ~/md_projects/<project>/ inside WSL. Never run large simulations on /mnt/c (slow I/O).
Use subdirectories: top/, em/, nvt/, npt/, md/, analysis/.

3. Build topology and solvate (per system type)

Protein/peptide: gmx pdb2gmx with the chosen force field; check termini, disulfides, and missing atoms.
Protein-ligand: parameterize the ligand first (acpype/GAFF2 for AMBER, CGenFF for CHARMM), merge with the protein, and verify residue names/charges.
Nucleic acid: pdb2gmx supports DNA/RNA with AMBER or CHARMM force fields.
Membrane: prepare with CHARMM-GUI or insane.py, then follow the membrane notes in references/workflow.md.

Then run editconf -d 1.0, solvate, and genion (neutralize, default 0.15 M NaCl). See references/workflow.md for exact commands.

4. Energy minimization

grompp with assets/templates/em.mdp, then mdrun.
Acceptance: potential energy negative and converged (Fmax < 1000 kJ/mol/nm), no LINCS warnings.

5. Equilibration

NVT (100 ps) then NPT (100 ps) with position restraints on heavy atoms.
Use assets/templates/nvt.mdp and npt.mdp; adjust tc-grps to the actual groups in the system.
Acceptance: temperature and pressure stable near targets, no explosions.

6. Production MD

Use assets/templates/md.mdp; set nsteps for the requested time.
Run on GPU:

gmx mdrun -deffnm md -nb gpu -pme gpu -update gpu -bonded gpu

Drop -bonded gpu for systems without GPU-supported bonded types.
Check the first ~1 ns: energy, temperature, pressure, RMSD drift.

7. Analysis

Core analyses: gmx rms, rmsf, gyrate, hbond, energy, distances/contacts.
Free-energy methods (umbrella sampling, gmx_MMPBSA, FEP) only when explicitly requested; confirm with the user because they are long and method-sensitive.
Produce plots (matplotlib or xmgrace). Verify convergence before interpreting.

8. Report

Summarize: system, protocol (force field, water model, ions, time), GPU performance, key results (RMSD/RMSF/Rg/hydrogen bonds), equilibrium status, and caveats. Suggest next steps.

Rules

Never fabricate results; only report numbers from actual output files.
Validate every mdrun completion: check for Finished mdrun and scan the log for fatal warnings.
Scientific validity matters: ask when the force field or other choices would materially change the result.
Keep raw trajectories (.xtc) and logs; all analysis must be reproducible.

Resources

references/workflow.md - detailed commands per system type, recipes, and common errors
assets/templates/*.mdp - ready-to-use EM/NVT/NPT/production parameter files

---name: gromacs-mddescription: Automate GROMACS molecular dynamics (MD) simulations end-to-end. Use when the user wants to set up, run, debug, or analyze MD simulations with GROMACS/gmx, including protein, protein-ligand, peptide, nucleic-acid, or membrane systems; build topologies and .mdp files; run pdb2gmx, solvate, genion, grompp, mdrun; perform energy minimization, NVT/NPT equilibration, and production runs with GPU acceleration; analyze trajectories (RMSD, RMSF, Rg, hydrogen bonds, contacts, free energy); or troubleshoot GROMACS errors. Also triggered by Chinese requests containing GROMACS, gmx, or 分子动力学模拟, and Japanese requests containing 分子動力学シミュレーション.---# GROMACS MD Automation## GoalTake a user's system description and structure, then run a scientifically sound GROMACS MD simulation with minimal back-and-forth and report the results.## LanguageUsers may write in Chinese (中文), English, or Japanese (日本語). Respond in the language the user uses.## Workflow### 0. Collect inputs (ask only for what is missing)- System type: protein / protein-ligand / nucleic acid / membrane / other- Structure: PDB ID, PDB file, or ligand SMILES/SDF (sequence-only -> suggest AlphaFold modeling first)- Goal: stability, conformational change, binding, free energy, etc.- Optional preferences: force field, water model, temperature (default 310 K), simulation length (default 100 ns), salt concentrationSee references/workflow.md for the input table and default choices. Do not block on optional preferences; use the defaults.### 1. Verify environmentRun:- `gmx --version` (expect `GPU support: CUDA` and GROMACS >= 2024)- `nvidia-smi` (GPU visible)If missing or broken, fix the environment first (references/workflow.md, Environment section).### 2. Create the project directory- Create `~/md_projects/<project>/` inside WSL. Never run large simulations on `/mnt/c` (slow I/O).- Use subdirectories: `top/`, `em/`, `nvt/`, `npt/`, `md/`, `analysis/`.### 3. Build topology and solvate (per system type)- Protein/peptide: `gmx pdb2gmx` with the chosen force field; check termini, disulfides, and missing atoms.- Protein-ligand: parameterize the ligand first (acpype/GAFF2 for AMBER, CGenFF for CHARMM), merge with the protein, and verify residue names/charges.- Nucleic acid: `pdb2gmx` supports DNA/RNA with AMBER or CHARMM force fields.- Membrane: prepare with CHARMM-GUI or insane.py, then follow the membrane notes in references/workflow.md.Then run `editconf -d 1.0`, `solvate`, and `genion` (neutralize, default 0.15 M NaCl). See references/workflow.md for exact commands.### 4. Energy minimization- `grompp` with assets/templates/em.mdp, then `mdrun`.- Acceptance: potential energy negative and converged (Fmax < 1000 kJ/mol/nm), no LINCS warnings.### 5. Equilibration- NVT (100 ps) then NPT (100 ps) with position restraints on heavy atoms.- Use assets/templates/nvt.mdp and npt.mdp; adjust `tc-grps` to the actual groups in the system.- Acceptance: temperature and pressure stable near targets, no explosions.### 6. Production MD- Use assets/templates/md.mdp; set `nsteps` for the requested time.- Run on GPU:```bashgmx mdrun -deffnm md -nb gpu -pme gpu -update gpu -bonded gpu```- Drop `-bonded gpu` for systems without GPU-supported bonded types.- Check the first ~1 ns: energy, temperature, pressure, RMSD drift.### 7. Analysis- Core analyses: `gmx rms`, `rmsf`, `gyrate`, `hbond`, `energy`, distances/contacts.- Free-energy methods (umbrella sampling, gmx_MMPBSA, FEP) only when explicitly requested; confirm with the user because they are long and method-sensitive.- Produce plots (matplotlib or xmgrace). Verify convergence before interpreting.### 8. ReportSummarize: system, protocol (force field, water model, ions, time), GPU performance, key results (RMSD/RMSF/Rg/hydrogen bonds), equilibrium status, and caveats. Suggest next steps.## Rules- Never fabricate results; only report numbers from actual output files.- Validate every `mdrun` completion: check for `Finished mdrun` and scan the log for fatal warnings.- Scientific validity matters: ask when the force field or other choices would materially change the result.- Keep raw trajectories (.xtc) and logs; all analysis must be reproducible.## Resources- references/workflow.md - detailed commands per system type, recipes, and common errors- assets/templates/*.mdp - ready-to-use EM/NVT/NPT/production parameter files

Frequently asked questions