gromacs-md-executor

name	gromacs-md-executor
description	GROMACS molecular dynamics skill for nanoparticle-biomolecule interaction simulations
allowed-tools	["Read","Write","Glob","Grep","Bash"]
metadata	{"specialization":"nanotechnology","domain":"science","category":"computational","priority":"medium","phase":6,"tools-libraries":["GROMACS","gmx_MMPBSA","MDAnalysis"]}

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

{
  "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"
}