# Alignments and RMS fitting¶

The MDAnalysis.analysis.align and MDAnalysis.analysis.rms modules contain the functions used for aligning structures, aligning trajectories, and calculating root mean squared quantities.

Note

These modules use the fast QCP algorithm to calculate the root mean square distance (RMSD) between two coordinate sets [The05] and the rotation matrix R that minimizes the RMSD [LAT09]. Please cite these references when using these modules.