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claude-codescience

Babysitter gromacs-biosim-runner

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

install
source · Clone the upstream repo
git clone https://github.com/a5c-ai/babysitter
Claude Code · Install into ~/.claude/skills/
T=$(mktemp -d) && git clone --depth=1 https://github.com/a5c-ai/babysitter "$T" && mkdir -p ~/.claude/skills && cp -r "$T/library/specializations/domains/science/physics/skills/gromacs-biosim-runner" ~/.claude/skills/a5c-ai-babysitter-gromacs-biosim-runner && rm -rf "$T"
manifest: library/specializations/domains/science/physics/skills/gromacs-biosim-runner/SKILL.md
tags
#molecular-dynamics#biomolecular#proteins#free-energy#simulation#gromacs
source content

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