Frequently asked questions


Why do the atom positions change over trajectories?

A fundamental concept in MDAnalysis is that at any one time, only one time frame of the trajectory is being accessed. The trajectory attribute of a Universe is actually (usually) a file reader. Think of the trajectory as a function \(X(t)\) of the frame index \(t\) that makes the data from this specific frame available. This structure is important because it allows MDAnalysis to work with trajectory files too large to fit into the computer’s memory. See Trajectories for more information.