gromacs-biosim-runner

# 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