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molecular-dynamics

Runs and analyzes molecular dynamics simulations using OpenMM and MDAnalysis. Covers system preparation with PDBFixer and OpenFF/GAFF2, force field choice (AMBER14, CHARMM36m, ff19SB), energy minimization, NVT/NPT equilibration, production MD, and trajectory analysis (RMSD, RMSF, protein-ligand contacts). Use when simulating a protein or protein-ligand system on GPU, assessing how a mutation affects protein dynamics, characterizing ligand binding mode, quantifying per-residue flexibility, or modeling membrane proteins and disordered proteins. Not for GROMACS or NAMD workflows, which the skill lists only as alternatives.

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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