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Yutong Zhao, Fu Kit Sheong, Jian Sun, Pedro Sander and Xuhui Huang A fast parallel clustering algorithm for molecular simulation trajectories Journal of Computational Chemistry 34

Version of Record online: 20 SEP 2012 | DOI: 10.1002/jcc.23110

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A GPU-powered parallel k-centers algorithm is able to speedup the clustering of molecular dynamics simulation conformations by up to two orders of magnitude compared to the CPU implementation. For example, it is capable of grouping 250,000 conformations of the Maltose Binding Protein (∼370 residues) into 4000 clusters within 40 s. To achieve this, the code on the GPU is effectively parallelized and the triangle inequality of metric spaces is utilized.

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