MDAnalysis is a Python library to analyze molecular dynamics trajectories
MDAnalysis is an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats. It can write most of these formats, too, together with atom selections suitable for visualization or native analysis tools. MDAnalysis allows one to read particle-based trajectories (including individual coordinate frames such as biomolecules in the PDB format) and access the atomic coordinates through NumPy arrays. This provides a flexible and relatively fast framework for complex analysis tasks. In addition, powerful atom selection commands are implemented. Trajectories can also be manipulated (for instance, fit to a reference structure) and written out.
- Molecular Dynamics