In analyze_foldamers, we have implemented clustering based on two different metrics: root-mean-square deviation (RMSD) of particle coordinates, and distance of the vector of backbone torsion angles. In the full coordinate RMSD approach, structures from all uncorrelated frames in the trajectory are first superimposed to an arbitrary reference frame using a rotational and translational optimization scheme. For each pair of frames, the coordinate RMSD distance matrix is the following: