Journal
COMPUTER PHYSICS COMMUNICATIONS
Volume 184, Issue 2, Pages 374-380Publisher
ELSEVIER
DOI: 10.1016/j.cpc.2012.09.022
Keywords
Molecular dynamics; Graphic processing unit; Accelerator; Precision model; SPSP; SPDP; DPDP; SPFP
Funding
- National Science Foundation [NSF1047875, NSF1148276]
- University of California [UC Lab 09-LR-06-117792]
- San Diego Supercomputer Center through National Science Foundation [TG-MCB090110]
- CUDA from NVIDIA
- Amazon Web Services
- Direct For Computer & Info Scie & Enginr
- Office of Advanced Cyberinfrastructure (OAC) [0910735] Funding Source: National Science Foundation
- Direct For Computer & Info Scie & Enginr
- Office of Advanced Cyberinfrastructure (OAC) [1148276] Funding Source: National Science Foundation
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A new precision model is proposed for the acceleration of all-atom classical molecular dynamics (MD) simulations on graphics processing units (GPUs). This precision model replaces double precision arithmetic with fixed point integer arithmetic for the accumulation of force components as compared to a previously introduced model that uses mixed single/double precision arithmetic. This significantly boosts performance on modern GPU hardware without sacrificing numerical accuracy. We present an implementation for NVIDIA GPUs of both generalized Born implicit solvent simulations as well as explicit solvent simulations using the particle mesh Ewald (PME) algorithm for long-range electrostatics using this precision model. Tests demonstrate both the performance of this implementation as well as its numerical stability for constant energy and constant temperature biomolecular MD as compared to a double precision CPU implementation and double and mixed single/double precision GPU implementations. (C) 2012 Elsevier B.V. All rights reserved.
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