ReddRadar
Agent skill
gromacs-biosim-runner
GROMACS molecular dynamics skill specialized for biomolecular systems, protein simulations, and free energy calculations
Install this agent skill to your Project
npx add-skill https://github.com/a5c-ai/babysitter/tree/main/library/specializations/domains/science/physics/skills/gromacs-biosim-runner
Metadata
Additional technical details for this skill
- tags
-
molecular-dynamics biomolecular proteins free-energy
- version
- 1.0
- category
- physics
SKILL.md
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
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