title: An improved method for nonbonded list generation: rapid determination of near-neighbor pairs.
abstract: 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 approximately 2.5 for a molecule of 5000 atoms with a cutoff in the 10 A range is obtained on Hewlett-Packard (HP) and Alpha processors, without greatly increasing memory requirements.
authors.affiliation: Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA. marci@tammy.harvard.edu
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Petrella
authors.forename: Ioan
authors.initials: I
authors.lastname: Andricioaei
authors.forename: Bernard R
authors.initials: BR
authors.lastname: Brooks
authors.forename: Martin
authors.initials: M
authors.lastname: Karplus
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D008962:Models, Theoretical