ReddRadar
Agent skill
gromacs-md-executor
GROMACS molecular dynamics skill for nanoparticle-biomolecule interaction simulations
Install this agent skill to your Project
npx add-skill https://github.com/a5c-ai/babysitter/tree/main/library/specializations/domains/science/nanotechnology/skills/gromacs-md-executor
Metadata
Additional technical details for this skill
- phase
- 6
- domain
- science
- category
- computational
- priority
- medium
- specialization
- nanotechnology
- tools libraries
-
[ "GROMACS", "gmx_MMPBSA", "MDAnalysis" ]
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"
}
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