In practice, we generate conformational datasets using WTmetaD simulations. Using PAk on configurations sampled from a WTmetaD simulation produces densities that reflect a probability distribution perturbed by the Cluster centers generated from smaller amounts of data (shown in red) are paired to the nearest cluster center in the reference set, allowing comparison of distances and energy differences between cluster centers. It is expected that as dataset size grow, the positions and energies of the cluster centers will converge, as seen in Fig. .