Universe - MDAnalysis/mdanalysis GitHub Wiki

The Universe class represents a whole simulation system. It is constructed from a topology (describing atom types and possibly connectivity) and a trajectory (the coordinates of the individual atoms, possibly as a function of time).

Almost every MDAnalysis script starts with

import MDAnalysis
u = MDAnalysis.Universe(topology, trajectory)

The object u encapsulates (almost) everything that MDAnalysis can do with a simulation system.