An improved method for nonbonded list generation: Rapid determination of near‐neighbor pairs

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