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An improved method for nonbonded list generation: Rapid determination of near‐neighbor pairs
Author(s) -
Petrella Robert J.,
Andricioaei Ioan,
Brooks Bernard R.,
Karplus Martin
Publication year - 2002
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.10123
Subject(s) - cutoff , range (aeronautics) , computer science , key (lock) , energy (signal processing) , feature (linguistics) , molecule , algorithm , materials science , physics , quantum mechanics , linguistics , philosophy , computer security , composite material
Generation of the list of near‐neighbor pairs of atoms not bonded to each other is a key feature of many programs for calculating the energy and energy derivatives for large molecules. Because this step can take a significant amount of CPU time, more efficient nonbonded list generation can speed up the energy calculations. In this article, a novel nonbonded list generation algorithm, BYCC, is introduced. It combines certain features of other algorithms and achieves more rapid nonbonded list generation; a factor of ≈2.5 for a molecule of 5000 atoms with a cutoff in the 10 Å range is obtained on Hewlett‐Packard (HP) and Alpha processors, without greatly increasing memory requirements. © 2002 Wiley Periodicals, Inc. J Comput Chem 24: 222–231, 2003