## Comparison of the three test ensembles using a method which involves dimensionality reduction and kernel density estimation.

A: Average residual stress according to Eq. 8 over 5 independent SPE projections of the three test ensembles. The standard deviation is smaller than the symbols shown. B: Example of a two-dimensional projection of the three ensembles. Each point represents an individual conformation, and the distance between each point is locally approximately the same as the RMSD between those two conformations. The two axes represent the two dimensions in the subspace of the SPE projection. C: Contour plots of the two-dimensional kernel estimates of the densities corresponding to the points in panel B. The grey bars next to the plots indicate the scale of the probability densities. D: Average and standard deviation of the Jensen-Shannon divergence between the three ensembles calculated using the kernel density estimates. The results are shown for different values of the dimensionality of the projections.