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.