Babysitter gromacs-md-executor

GROMACS molecular dynamics skill for nanoparticle-biomolecule interaction simulations

install

source · Clone the upstream repo

git clone https://github.com/a5c-ai/babysitter

Claude Code · Install into ~/.claude/skills/

T=$(mktemp -d) && git clone --depth=1 https://github.com/a5c-ai/babysitter "$T" && mkdir -p ~/.claude/skills && cp -r "$T/library/specializations/domains/science/nanotechnology/skills/gromacs-md-executor" ~/.claude/skills/a5c-ai-babysitter-gromacs-md-executor && rm -rf "$T"

manifest: library/specializations/domains/science/nanotechnology/skills/gromacs-md-executor/SKILL.md

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

System Preparation
- Parameterize nanoparticle
- Solvate system
- Add ions for neutralization
Equilibration
- Minimize energy
- NVT equilibration
- NPT equilibration
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"
}