Clustering is a popular technique for partitioning MD simulations, it has been used to find representative structures based on the protein geometry . We demonstrate an alternative approach: using the 𝐸𝐸 "⃗ (𝑟𝑟) streamline distribution to find representative clusters of 𝐸𝐸 "⃗ (𝑟𝑟) configurations, rather than atomic positions. PyCPET can compute the 𝐸𝐸 "⃗ (𝑟𝑟) streamline distribution at each frame of an MD trajectory (Figure ), and then uses the χ ! distance (Eq. 3 in Methods) to construct a pairwise distance matrix, and perform K-Medoids clustering to obtain representative structures.