gromacs-md-executor

# GROMACS MD Executor ## Purpose The GROMACS MD Executor skill provides molecular dynamics simulation capabilities specialized for nanoparticle-biomolecule interactions, enabling investigation of drug delivery systems, protein-surface interactions, and membrane penetration. ## Capabilities - Nanoparticle-protein simulations - Membrane-nanoparticle interactions - Coarse-grained modeling (Martini) - Free energy calculations - Enhanced sampling methods - Trajectory analysis and visualization ## Usage Guidelines ### Bio-Nano MD Workflow 1. **System Preparation** - Parameterize nanoparticle - Solvate system - Add ions for neutralization 2. **Equilibration** - Minimize energy - NVT equilibration - NPT equilibration 3. **Production and Analysis** - Run appropriate sampling - Calculate binding energies - Analyze interactions ## Process Integration - Molecular Dynamics Simulation Workflow - Nanoparticle Drug Delivery System Development ## Input Schema ```json { "nanoparticle_file": "string", "biomolecule_file": "string", "force_field": "CHARMM36|AMBER|Martini", "simulation_type": "binding|membrane|protein_corona", "temperature": "number (K)", "simulation_time": "number (ns)" } ``` ## Output Schema ```json { "binding_energy": "number (kJ/mol)", "contact_residues": ["string"], "rmsd": "number (nm)", "interaction_analysis": { "hydrogen_bonds": "number", "hydrophobic_contacts": "number" }, "trajectory_file": "string...