Efficient Maintenance and Update of Nonbonded Lists in Macromolecular Simulations.

ABSTRACT: Molecular mechanics and dynamics simulations use distance based cutoff approximations for faster computation of pairwise van der Waals and electrostatic energy terms. These approximations traditionally use a precalculated and periodically updated list of interacting atom pairs, known as the "nonbonded neighborhood lists" or nblists, in order to reduce the overhead of finding atom pairs that are within distance cutoff. The size of nblists grows linearly with the number of atoms in the system and superlinearly with the distance cutoff, and as a result, they require significant amount of memory for large molecular systems. The high space usage leads to poor cache performance, which slows computation for large distance cutoffs. Also, the high cost of updates means that one cannot afford to kee

SUBMITTER: Chowdhury R 

PROVIDER: S-EPMC4196749 | biostudies-literature | 2014 Oct

REPOSITORIES: biostudies-literature