Individual skill
molecular-dynamics
Run and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Set up protein/small molecule systems, define force fields, run energy minimization and production MD, analyze trajectories (RMSD, RMSF, contact maps, free energy surfaces). For structural biology, drug binding, and biophysics.
backend/cli/skills/chemistry/molecular-dynamics/SKILL.md
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# Molecular Dynamics
## Overview
Molecular dynamics (MD) simulation computationally models the time evolution of molecular systems by integrating Newton's equations of motion. This skill covers two complementary tools:
- **OpenMM** (https://openmm.org/): High-performance MD simulation engine with GPU support, Python API, and flexible force field support
- **MDAnalysis** (https://mdanalysis.org/): Python library for reading, writing, and analyzing MD trajectories from all major simulation packages
**Installation:**
```bash
conda install -c conda-forge openmm mdanalysis nglview
# or
uv pip install openmm mdanalysis