title: GPU/CPU Algorithm for Generalized Born/Solvent-Accessible Surface Area Implicit Solvent Calculations.
abstract: 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 demonstrated here are generally applicable to parallel applications employing hybrid GPU/CPU calculations.
authors.affiliation: Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign  ; Beckman Institute, University of Illinois at Urbana-Champaign.
authors.forename: David E
authors.initials: DE
authors.lastname: Tanner
authors.forename: James C
authors.initials: JC
authors.lastname: Phillips
authors.forename: Klaus
authors.initials: K
authors.lastname: Schulten