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Algorithms for clustering molecular dynamics configurations
Author(s) -
Torda Andrew E.,
van Gunsteren Wilfred F.
Publication year - 1994
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.540151203
Subject(s) - cluster analysis , maxima and minima , centroid , molecular dynamics , cluster (spacecraft) , hierarchical clustering , hierarchy , computer science , algorithm , linkage (software) , trajectory , space (punctuation) , data mining , mathematics , artificial intelligence , computational chemistry , physics , chemistry , mathematical analysis , biochemistry , astronomy , economics , market economy , gene , programming language , operating system
Two traditional clustering algorithms are applied to configurations from a long molecular dynamics trajectory and compared using two sets of test data. First, a subset of atoms was chosen to present conformations which naturally fall into a number of clusters. Second, a subset of atoms was selected to span a relatively continuous region of conformational space rather than form discrete conformational classes. Of the two algorithms used, the single linkage method is inappropriate for this kind of data. The divisive hierarchical method, based on minimizing the difference between cluster centroids and extrema, is successful but also prone to imposing clustering hierarchy where none can be justified. © 1994 by John Wiley & Sons, Inc.