molecular-dynamics

Run and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Set up protein and protein-ligand systems with PDBFixer, choose force fields and water models (AMBER14, CHARMM36m, ff19SB, GAFF2, TIP3P), solvate and add ions, run energy minimization, NVT/NPT equilibration and production MD on GPU, then analyze trajectories for RMSD, RMSF, radius of gyration, hydrogen bonds, native contacts, PCA and free energy surfaces. Use this skill for protein stability under mutation, ligand binding-mode and residence-time questions, conformational sampling, membrane proteins, and disordered ensembles. Also trigger on OpenMM, MDAnalysis, mdtraj, Simulation.step, LangevinMiddleIntegrator, PDBFixer, DCD or XTC trajectory, RMSD analysis, or production MD.

Version

1.2

License

MIT

Compatibility

Requires Python 3.11+ with openmm and mdanalysis, best installed from conda-forge; PDBFixer and nglview are optional extras. A CUDA or OpenCL GPU is effectively required — production MD on CPU is 10-100x slower, so nanoseconds become days. Trajectory analysis alone runs fine on CPU.