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:** ```bash conda install -c conda-forge openmm mdanalysis nglview # or pip install openmm mdanalysis ``` ## 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 binding energetics - **RMSD/RMSF analysis**: Quantify structural fluctuations from a reference structure - **Free energy estimation**: Compute binding free energy or conformational free energy - **Membrane simulations**: Model proteins in lipid bilayers - **Intrinsically disordered proteins**: Study IDR conformational ensembles ## Core Workflow: OpenMM Simulation ### 1. System Preparation ```python from openmm.app import * from openmm import * from openmm.unit import * import sys def prepa...