# Gromacs Biosim Runner

> GROMACS molecular dynamics skill specialized for biomolecular systems, protein simulations, and free energy calculations

- Skill: `a5c-ai/gromacs-biosim-runner` (Agent Skill)
- Install (CLI): `npx skillmds@latest add a5c-ai/gromacs-biosim-runner`
- Raw SKILL.md: https://api.skillmd.com/api/skills/a5c-ai/gromacs-biosim-runner/raw
- Safety review: pending (external: skill-scanner PASS, skillspector PASS)
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: a5c-ai (https://skillmd.com/u/a5c-ai)
- Updated: 2026-09-09
- Page: https://skillmd.com/skills/a5c-ai/gromacs-biosim-runner

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# 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