GROMACS molecular dynamics skill specialized for biomolecular systems, protein simulations, and free energy calculations
name gromacs-biosim-runner description GROMACS molecular dynamics skill specialized for biomolecular systems, protein simulations, and free energy calculations allowed-tools ["Read","Write","Glob","Grep","Edit","WebFetch","WebSearch","Bash"] metadata {"version":"1.0","category":"physics","tags":["molecular-dynamics","biomolecular","proteins","free-energy"]} 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