GROMACS Biosim Runner Skill

SkillDev tools

GROMACS molecular dynamics skill specialized for biomolecular systems, protein simulations, and free energy calculations

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 Biosim Runner Skill skill

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: 112
Last commit: Sep 2026

Advanced

Item type: skill
Key: gromacs-biosim-runner
Source: github.com/a5c-ai/babysitter

github.com/a5c-ai/babysitter