Combining cluster energetic information with RM SD cluster illustrates the potential energy landscape about each identified cluster. In figure we can see two minimum energy clusters are identified along with two higher energy clusters. In this example, the two minimum energy cluster corresponds to a left and right handed-helix. The groups of points near 0.08 and 0.12 RMSD away from the minimum energy structure represent structures with frayed helix ends. Figure : An example RMSD from cluster minimum energy structures to individual cluster structures vs energy plot for each cluster for a given parameter set. For each cluster the minimum energy structure will have an RMSD of 0 and will be the lowest identified energy of its respective cluster. Cluster 0 and 1 are the degenerate minimum energy clusters identified in this parameter scan. Clusters 2-4 represent higher energy minima found while searching this potential energy landscape. Gaps in the RMSD distribution of each cluster are the result of discrete unfolding events of 1-2 residues. Note carefully that distance along the horizontal axis represents distance from the cluster minima to each structure, not the distance between clusters.