Repository: Freie Universität Berlin, Math Department

Comparing geometric and kinetic cluster algorithms for molecular simulation data

Xavier , D. and Keller, B. and van Gunsteren, W. F. (2010) Comparing geometric and kinetic cluster algorithms for molecular simulation data. J. Chem. Phys., 132 (7). 074110.

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The identification of metastable states of a molecule plays an important role in the interpretation of molecular simulation data because the free-energy surface, 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 geometric cluster algorithm - 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 geometric cluster algorithms using five two-dimensional data sets. Second, we analyze the molecular dynamics data of beta-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 geometric clustering strongly depends on the algorithm used and that the density based common-nearest-neighbor algorithm is the most robust of the three geometric cluster algorithms with respect to variations in the input parameters and the distance metric. When comparing the geometric cluster results to the metastable states of the beta-heptapeptide as identified by kinetic clustering, we find that in most cases the folded state is identified correctly but the overlap of geometric clusters with further metastable states is often at best approximate.

Item Type:Article
Subjects:Physical Sciences > Physics > Mathematical & Theoretical Physics > Computational Physics
Physical Sciences > Chemistry > Physical Chemistry
Biological Sciences > Molecular Biology
Physical Sciences > Physics > Chemical Physics
ID Code:839
Deposited By: BioComp Admin
Deposited On:12 Mar 2010 11:37
Last Modified:27 Oct 2010 11:47

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