A simple method for faster nonbonded force evaluations.
Accurate approximations are introduced for the evaluation of inverse interparticle distances such that square root or division operations are not required in the computation of interparticle interactions and forces. These generally applicable approximations are illustrated by incorporation into the protein simulation package TINKER along with several other speed enhancement strategies. With these modifications, implicit solvent Langevin dynamics simulations of proteins are performed factors of 4.6 times faster than the modified open source distributed program. Programming speedups are obtained by extensive vectorization, simplification of the inner loop to avoid IF statements, and by using lookup tables for the distance dependent "dielectric constant" in implicit solvent models. Benchmarks are provided for the all-atom, implicit solvent dynamics of Met-enkephalin, the villin headpiece, the B1 domain of protein-G, and barnase. We also discuss the more general applicability of the approximation methods to explicit solvent simulations and of look-up tables for other implicit solvent models such as the generalized Born models.
Shen
Min-Yi
MY
The James Franck Institute and Department of Chemistry, The University of Chicago, 5640 S. Ellis Avenue, Chicago, Illinois 60637, USA.
Freed
Karl F
KF
D000465:Algorithms; D001426:Bacterial Proteins; D003198:Computer Simulation; D004744:Enkephalin, Methionine / Q000737:chemistry; D019204:GTP-Binding Proteins / Q000737:chemistry; D008840:Microfilament Proteins / Q000737:chemistry; D008958:Models, Molecular; D011506:Proteins / Q000737:chemistry*; D012260:Ribonucleases / Q000737:chemistry; D013816:Thermodynamics
D001426:Bacterial Proteins; D008840:Microfilament Proteins; D011506:Proteins; C026615:villin; D004744:Enkephalin, Methionine; D012260:Ribonucleases; C019760:Bacillus amyloliquefaciens ribonuclease; D019204:GTP-Binding Proteins