title: Parallelization and improvements of the generalized born model with a simple sWitching function for modern graphics processors.
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 studies of peptides and potentially small proteins.
authors.affiliation: Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan, 48109.
authors.forename: Evan J
authors.initials: EJ
authors.lastname: Arthur
authors.affiliation: Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan, 48109.|LSA Biophysics, University of Michigan, 930 N. University Ave, Ann Arbor, Michigan, 48109.
authors.forename: Charles L
authors.initials: CL
authors.lastname: Brooks
mesh_terms: D000465:Algorithms; D056004:Molecular Dynamics Simulation; D009842:Oligopeptides / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D009842:Oligopeptides; C506175:chignolin
keywords: CHARMM; CUDA; GPU; OpenMM; chignolin; graphic processing unit; implicit solvation; parallelization; protein folding; solvation; solvent model