Individual skill
gromacs-biosim-runner
GROMACS molecular dynamics skill specialized for biomolecular systems, protein simulations, and free energy calculations
library/specializations/domains/science/physics/skills/gromacs-biosim-runner/SKILL.md
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- Nov 1, 2026
- License
- MIT
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- molecular-dynamics Declared skill tag
- biomolecular Declared skill tag
- proteins Declared skill tag
- free-energy Declared skill tag
- engineering Derived category
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# GROMACS Biosim Runner Skill
## 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