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 versions: OpenMM 8.x, MDAnalysis 2.x):

# uv (preferred) — both ship binary wheels for arm64 macOS, no conda needed
uv add openmm "mdanalysis>=2.9" pdbfixer
# pdbfixer is not on PyPI for all platforms; if the wheel is unavailable:
uv pip install "pdbfixer @ git+https://github.com/openmm/pdbfixer.git"