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Comparing geometric and kinetic cluster algorithms for molecular simulation data

B. Keller, X. Daura, W. F. van Gunsteren – 2010

The identification of metastable states of a molecule plays an important role in the interpretation of molecular simulation data because the free-energysurface, the relative populations in this landscape, and ultimately also the dynamics of the molecule under study can be described in terms of these states. We compare the results of three different geometriccluster algorithms (neighbor algorithm, K-medoids algorithm, and common-nearest-neighbor algorithm) among each other and to the results of a kinetic cluster algorithm. First, we demonstrate the characteristics of each of the geometriccluster algorithms using five two-dimensional data sets. Second, we analyze the molecular dynamics data of a β-heptapeptide in methanol—a molecule that exhibits a distinct folded state, a structurally diverse unfolded state, and a fast folding/unfolding equilibrium—using both geometric and kinetic cluster algorithms. We find that geometricclustering strongly depends on the algorithm used and that the density based common-nearest-neighbor algorithm is the most robust of the three geometriccluster algorithms with respect to variations in the input parameters and the distance metric. When comparing the geometriccluster results to the metastable states of the β-heptapeptide as identified by kinetic clustering, we find that in most cases the folded state is identified correctly but the overlap of geometricclusters with further metastable states is often at best approximate.

Comparing geometric and kinetic cluster algorithms for molecular simulation data
B. Keller, X. Daura, W. F. van Gunsteren
DOI 10.1063/1.3301140
J. Chem. Phys., 132 (2010), p. 074110