Molecular Dynamics

---
name: molecular-dynamics
description: 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.
license: MIT
metadata: {"version": "1.0", "skill-author": "Kuan-lin Huang"}
---

# 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
pip install openmm mdanalysis
```

## When to Use This Skill
… load the full skill through Skill Me