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gromacs-md-executor

// GROMACS molecular dynamics skill for nanoparticle-biomolecule interaction simulations

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updated:March 4, 2026
SKILL.mdreadonly
SKILL.md Frontmatter
namegromacs-md-executor
descriptionGROMACS molecular dynamics skill for nanoparticle-biomolecule interaction simulations
allowed-toolsRead,Write,Glob,Grep,Bash
metadata[object Object]

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"
}