alterlab-molecular-dynamics

# 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): ```bash # 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" # conda-forge alternative (pulls CUDA builds on Linux): # conda install -c conda-forge openmm mdanalysis pdbfixer nglview ``` Note: on Apple Silicon there is no CUDA; OpenMM falls back to the `CPU` (and, on macOS, `OpenCL`/Metal) platforms — see the platform-selection block below. ## When to Use This Skill Use molecular dynamics when: - **Protein stability analysis**: How does a mutation affect protein dynamics? - **Drug binding simulations**: Characterize binding mode and residence time of a ligand - **Conformational sampling**: Explore protein flexibility and conformational changes - **Protein-protein interaction**: Model interface dynamics and...