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Fast lookup tables for interatomic interactions
Author(s) -
Hunt Nathan G.,
Cohen Fred E.
Publication year - 1996
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/(sici)1096-987x(199612)17:16<1857::aid-jcc6>3.0.co;2-m
Subject(s) - lookup table , computer science , speedup , table (database) , monte carlo method , pairwise comparison , algorithm , function (biology) , statistical physics , field (mathematics) , computational science , physics , parallel computing , mathematics , data mining , statistics , artificial intelligence , evolutionary biology , biology , pure mathematics , programming language
We describe novel lookup tables for the rapid calculation of interatomic interactions. The tables have nonuniform distributions of bin widths tailored to minimize numerical error and maximize computational speed. Since interaction energies are precalculated, computer time requirements are essentially independent of the form of the potential function used. In test calculations using the AMBER force field and an internal coordinate Monte Carlo algorithm, the lookup table runs 15% faster than direct calculation of nonbonded interactions. The method is more advantageous for more complicated energy functions. As an example of a more complicated potential function, we have tested a pairwise approximation to accessible surface area. In this case, the use of the lookup table results in a speedup of a factor of two. The method is straightforward to implement and should be widely applicable. © 1996 by John Wiley & Sons, Inc.