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: When to Use This Skill Use molecular dynamics when: - Protein stability analysis : How does a mu…