---
name: gromacs-md-executor-cfd43ecc02bf
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
graph:
  domains: [domain:nanotechnology]
  skillAreas: [skill-area:mathematical-reasoning, skill-area:physics-simulation, skill-area:data-analysis]
  workflows: [workflow:experiment-design]
  roles: [role:research-engineer]
---

# 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"
}
```


---
Source attribution: a5c-ai
Original project: https://github.com/a5c-ai/babysitter/blob/feb68abe397acc14f32b34984975c48fedba2b33/library/specializations/domains/science/nanotechnology/skills/gromacs-md-executor/SKILL.md
License: MIT
License information: https://opensource.org/license/mit
Original upstream instructions; downloaded from Mega AI Hub.

## Upstream license notice

# MIT License

Copyright (c) 2025 A5C AI

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.



# Mega AI Hub resource metadata

Creator / publisher: a5c-ai
Original project: https://github.com/a5c-ai/babysitter/blob/feb68abe397acc14f32b34984975c48fedba2b33/library/specializations/domains/science/nanotechnology/skills/gromacs-md-executor/SKILL.md
Attribution basis: Source repository record

Fields of work: Data & Analytics, Development & Engineering, Education & Research
Roles: Data Scientist, ML / AI Engineer, Researcher
Specialties: Specialty not specified
Tools: Gromacs, Mdanalysis, Gmx_Mmpbsa
Country applicability: Country not specified
Classification basis: Source catalog labels
Instruction SHA-256: c9f562ae61245ea0fe4c21ee8975efc526b89880580540b9fa0e31737337e838