GROMACS MD Executor
SkillDev toolsGROMACS molecular dynamics skill for nanoparticle-biomolecule interaction simulations
Instructions available. Your AI can read the instructions. Execution depends on the setup they require.
Account requirements not reviewed. Check the skill instructions before use; ahel provides instructions and does not run this skill.
Add ahel to your AI once: Claude, ChatGPT, Cursor, Claude Code or Codex. Then ask it to use this.
Then ask your AI: use the GROMACS MD Executor skill
What this skill tells your AI
The instructions your AI receives, as published by a5c-ai/babysitter in library/specializations/domains/science/nanotechnology/skills/gromacs-md-executor/SKILL.md and read by ahel’s review.
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"
}
Signals
- GitHub stars
- 2k
- Forks
- 112
- Last commit
- Sep 2026
Advanced
- Item type
- skill
- Key
gromacs-md-executor- Source
- github.com/a5c-ai/babysitter