Free SKILL.md scraped from GitHub. Clone the repo or copy the file directly into your Claude Code skills directory.
npx versuz@latest install a5c-ai-babysitter-library-specializations-domains-science-physics-skills-gromacs-bgit clone https://github.com/a5c-ai/babysitter.gitcp babysitter/SKILL.MD ~/.claude/skills/a5c-ai-babysitter-library-specializations-domains-science-physics-skills-gromacs-b/SKILL.md---
name: gromacs-biosim-runner
description: GROMACS molecular dynamics skill specialized for biomolecular systems, protein simulations, and free energy calculations
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metadata:
version: "1.0"
category: physics
tags:
- molecular-dynamics
- biomolecular
- proteins
- free-energy
---
# GROMACS Biosim Runner Skill
## Purpose
Provide specialized integration with GROMACS for biomolecular simulations including protein dynamics, free energy calculations, and enhanced sampling methods.
## Capabilities
- Topology preparation and solvation
- Energy minimization workflows
- NPT/NVT equilibration protocols
- Free energy perturbation setup
- Trajectory analysis (RMSD, RMSF, RDF)
- Enhanced sampling methods (metadynamics, replica exchange)
## Usage Guidelines
- Use appropriate water models (TIP3P, TIP4P, SPC/E)
- Select force fields compatible with target biomolecules (AMBER, CHARMM, OPLS)
- Follow standard equilibration protocols
- Monitor system stability during production runs
## Dependencies
- GROMACS
- pdb2gmx
- MDAnalysis
- PLUMED (for enhanced sampling)
## Process Integration
- Molecular Dynamics Simulation Setup
- High-Performance Computing Workflow