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Gromacs biosim runner

Skill a5c-ai/babysitter/library/specializations/domains/science/physics/skills/gromacs-biosim-runner

GROMACS molecular dynamics skill specialized for biomolecular systems, protein simulations, and free energy calculationsFrom its SKILL.md

Install
npx -y skills add a5c-ai/babysitter --skill gromacs-biosim-runner

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SKILL.md

1.5 KB, 202 tokens by cl100k_base, as published. Nobody here has run it

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

What ships with it

Read from the repository

Just SKILL.md. No reference files, no scripts.

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