gromacs-biosim-runner

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

General

What this skill does


# 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

Files: 1

Size: 1.3 KB

Complexity: 9/100

Category: General

Source: https://github.com/a5c-ai/babysitter/tree/main/library/specializations/domains/science/physics/skills/gromacs-biosim-runner

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