# Trajectory similarityΒΆ

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.