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
2. Parameterize nanoparticle
3. Solvate system
4. Add ions for neutralization

1. Equilibration
2. Minimize energy
3. NVT equilibration
4. NPT equilibration

1. Production and Analysis
2. Run appropriate sampling
3. Calculate binding energies
4. Analyze interactions

Process Integration

• Molecular Dynamics Simulation Workflow
• Nanoparticle Drug Delivery System Development

Input Schema

{
  "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

{
  "binding_energy": "number (kJ/mol)",
  "contact_residues": ["string"],
  "rmsd": "number (nm)",
  "interaction_analysis": {
    "hydrogen_bonds": "number",
    "hydrophobic_contacts": "number"
  },
  "trajectory_file": "string"
}