An improved method for nonbonded list generation: Rapid determination of near-neighbor pairs
✍ Scribed by Robert J. Petrella; Ioan Andricioaei; Bernard R. Brooks; Martin Karplus
- Publisher
- John Wiley and Sons
- Year
- 2002
- Tongue
- English
- Weight
- 162 KB
- Volume
- 24
- Category
- Article
- ISSN
- 0192-8651
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✦ Synopsis
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.