molecular-dynamics

You can run an end-to-end molecular dynamics workflow by preparing the system, selecting force fields, and performing energy minimization, NVT/NPT equilibration, and production MD. It integrates OpenMM for simulation execution and MDAnalysis for trajectory analysis.

Yes, MDAnalysis trajectory analysis supports protein stability and drug binding studies by computing RMSD, RMSF, contact maps, and free-energy estimations. These metrics reveal conformational changes and interaction details for protein–ligand systems.

The OpenMM MD workflow supports protein systems, protein–ligand binding, membrane proteins, and intrinsically disordered proteins. It enables conformational sampling and protein–protein interaction studies through production runs and trajectory analysis.

Yes, OpenMM handles both NVT and NPT equilibration phases. The workflow guides you through system preparation, force-field selection, and energy minimization before proceeding to equilibration and subsequent production MD runs.

You can compute RMSD, RMSF, and contact maps for intrinsically disordered proteins using MDAnalysis. These trajectory analysis metrics evaluate conformational sampling and structural dynamics specific to disordered systems.

Energy minimization removes steric clashes in the prepared system, while NVT/NPT equilibration stabilizes temperature and pressure. Both steps are required before production MD to ensure physically valid molecular dynamics trajectories.