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.


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