David E. Tanner, James C. Phillips, and Klaus Schulten.
GPU/CPU algorithm for generalized Born / solvent-accessible
surface area implicit solvent calculations.
Journal of Chemical Theory and Computation, 8:2521-2530, 2012.
(PMC: 3464051)
TANN2012
Molecular dynamics methodologies comprise a vital research tool for structural biology.
Molecular dynamics has benefited from technological advances in computing, such as
multi-core CPUs and graphics processing units (GPUs), but harnessing the full power of
hybrid GPU/CPU computers remains difficult. The generalized Born / solvent-accessible
surface area implicit solvent model (GB/SA) stands to benefit from hybrid GPU/CPU
computers, employing the GPU for the GB calculation and the CPU for the SA calculation.
Here, we explore the computational challenges facing GB/SA calculations on hybrid
GPU/CPU computers and demonstrate how NAMD, a parallel molecular dynamics program,
is able to efficiently utilize GPUs and CPUs simultaneously for fast GB/SA simulations. The
hybrid computation principles here demonstrated are generally applicable to parallel
applications employing hybrid GPU/CPU calculations.
Download Full Text
The manuscripts available on our site are provided for your personal
use only and may not be retransmitted or redistributed without written
permissions from the paper's publisher and author. You may not upload any
of this site's material to any public server, on-line service, network, or
bulletin board without prior written permission from the publisher and
author. You may not make copies for any commercial purpose. Reproduction
or storage of materials retrieved from this web site is subject to the
U.S. Copyright Act of 1976, Title 17 U.S.C.
