A molecular dynamics trajectory with \(N\) atoms can be considered through a path through \(3N\)-dimensional molecular configuration space. MDAnalysis contains a number of algorithms to compare the conformational ensembles of different trajectories. Most of these are in the
MDAnalysis.analysis.encore module ([TPB+15]) and compare estimated probability distributions to measure similarity. The path similarity analysis compares the RMSD between pairs of structures in conformation transition paths.
MDAnalysis.analysis.encore also contains functions for evaluating the conformational convergence of a trajectory using the similarity over conformation clusters or similarity in a reduced dimensional space.