molecular-dynamics

Runs and analyzes molecular dynamics simulations with OpenMM and MDAnalysis. Sets up protein/small molecule systems, defines force fields, runs energy minimization and production MD, and analyzes trajectories (RMSD, RMSF, contact maps, free energy surfaces). For structural biology, drug binding, and biophysics.

Version

1.3

License

MIT

Compatibility

Requires Python 3.11+ with OpenMM and MDAnalysis; matplotlib for plots. Optional PDBFixer and OpenFF need separate installation. Network access for installation; local simulation and analysis run offline.