Parallelization and improvements of the generalized born model with a simple sWitching function for modern graphics processors

Journal of Computational Chemistry
Evan J Arthur, Charles L Brooks

Abstract

Two fundamental challenges of simulating biologically relevant systems are the rapid calculation of the energy of solvation and the trajectory length of a given simulation. The Generalized Born model with a Simple sWitching function (GBSW) addresses these issues by using an efficient approximation of Poisson-Boltzmann (PB) theory to calculate each solute atom's free energy of solvation, the gradient of this potential, and the subsequent forces of solvation without the need for explicit solvent molecules. This study presents a parallel refactoring of the original GBSW algorithm and its implementation on newly available, low cost graphics chips with thousands of processing cores. Depending on the system size and nonbonded force cutoffs, the new GBSW algorithm offers speed increases of between one and two orders of magnitude over previous implementations while maintaining similar levels of accuracy. We find that much of the algorithm scales linearly with an increase of system size, which makes this water model cost effective for solvating large systems. Additionally, we utilize our GPU-accelerated GBSW model to fold the model system chignolin, and in doing so we demonstrate that these speed enhancements now make accessible folding...Continue Reading

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Citations

Oct 13, 2016·Journal of Chemical Theory and Computation·Melina K RobinsonM Scott Shell
Nov 20, 2016·Journal of Computational Chemistry·Sunhwan JoWonpil Im
Feb 6, 2017·Journal of Computational Chemistry·Baofeng ZhangEmilio Gallicchio
Mar 13, 2019·Annual Review of Biophysics·Alexey V Onufriev, David A Case
Jul 14, 2016·Journal of Computational Chemistry·Evan J Arthur, Charles L Brooks
Oct 11, 2017·Journal of Chemical Theory and Computation·Parimal Kar, Michael Feig
May 7, 2020·Journal of Chemical Information and Modeling·Dragos HorvathAlexandre Varnek
Sep 20, 2018·The Journal of Physical Chemistry. B·Peter J Steinbach
Dec 12, 2018·Journal of Chemical Theory and Computation·Jumin LeeWonpil Im

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