AgentSkillsCN

gromacs-md-executor

精通 GROMACS 分子动力学技术，可用于纳米颗粒与生物分子相互作用的模拟

SKILL.md
--- frontmatter
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

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"
}