molecular-dynamics

SUMMARY

What it does

This Agent Skill provides guidance and code examples for running and analyzing molecular dynamics (MD) simulations using OpenMM and MDAnalysis. It covers system preparation (e.g., adding hydrogens, solvation), energy minimization, NVT/NPT equilibration, production MD runs, and trajectory analysis including RMSD, RMSF, contact maps, and free energy surfaces. The skill is intended for structural biology, drug binding, and biophysics applications. Evidence is based on the SKILL.md source file, which includes detailed Python code snippets and best practices.