Clustering validation protocol. This diagram outlines the process of verifying the results of a clustering algorithm applied to molecular dynamics simulations. The model polymers have certain known properties (meta-stable states, transition states, etc.) that are known beforehand due to model construction. The statistics and features of clusters that describe these properties can then be used to inform the analysis of molecular dynamics simulations. If the properties displayed by the polymer models are also be present in the molecular dynamics simulations, then the statistics and features of the clusters will also share similarities. Any clustering algorithm could be used, but we focus on spectral clustering here.