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