Trajectory similarity
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 Comparing the geometric similarity of trajectories tutorial 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.