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) - Fo…