MDAnalysis documentation¶

MDAnalysis (www.mdanalysis.org) is an object-oriented python toolkit to analyze molecular dynamics trajectories generated by CHARMM, Gromacs, Amber, NAMD, LAMMPS, DL_POLY and other packages; it also reads other formats (e.g., PDB files and XYZ format trajectories; see Table of supported coordinate formats and Table of Supported Topology Formats for the full lists). It can write most of these formats, too, together with atom selections for use in Gromacs, CHARMM, VMD and PyMol (see Selection exporters).
It allows one to read molecular dynamics trajectories and access the atomic coordinates through NumPy arrays. This provides a flexible and relatively fast framework for complex analysis tasks. Fairly complete atom Selection commands are implemented. Trajectories can also be manipulated (for instance, fit to a reference structure) and written out in a range of formats.