GROMACS Biosim Runner Skill
SkillDev toolsGROMACS molecular dynamics skill specialized for biomolecular systems, protein simulations, and free energy calculations
Use GROMACS Biosim Runner Skill in Claude, ChatGPT or Ahel Desktop
Free. Sign in, add GROMACS Biosim Runner Skill and connect your AI. About a minute.
Also: Claude Code · Cursor · Codex
Then ask your AI: use the GROMACS Biosim Runner Skill
Details
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.
No other account needed.
Add Ahel to your AI once: Claude, ChatGPT, Cursor, Claude Code or Codex. Then ask it to use this.
What this skill tells your AI
The instructions your AI receives, as published by a5c-ai/babysitter in library/specializations/domains/science/physics/skills/gromacs-biosim-runner/SKILL.md and read by Ahel’s review.
Purpose
Provide specialized integration with GROMACS for biomolecular simulations including protein dynamics, free energy calculations, and enhanced sampling methods.
Capabilities
- Topology preparation and solvation
- Energy minimization workflows
- NPT/NVT equilibration protocols
- Free energy perturbation setup
- Trajectory analysis (RMSD, RMSF, RDF)
- Enhanced sampling methods (metadynamics, replica exchange)
Usage Guidelines
- Use appropriate water models (TIP3P, TIP4P, SPC/E)
- Select force fields compatible with target biomolecules (AMBER, CHARMM, OPLS)
- Follow standard equilibration protocols
- Monitor system stability during production runs
Dependencies
- GROMACS
- pdb2gmx
- MDAnalysis
- PLUMED (for enhanced sampling)
Process Integration
- Molecular Dynamics Simulation Setup
- High-Performance Computing Workflow
Signals
- GitHub stars
- 2k
- Forks
- 113
- Last commit
- Sep 2026
Advanced
- Item type
- skill
- Key
gromacs-biosim-runner- Source
- github.com/a5c-ai/babysitter