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 (verified as of 2026-09: OpenMM 8.6.1, MDAnalysis 2.10, pdbfixer 1.12):

# uv (preferred) — all three publish binary wheels on PyPI, no conda needed
uv add openmm "mdanalysis>=2.10" pdbfixer
# If a pdbfixer wheel is unavailable for your platform, install from source:
uv pip install "pdbfixer @ git+https://github.com/openmm/pdbfixer.git"