title: Accelerating electrostatic surface potential calculation with multi-scale approximation on graphics processing units.
abstract: Tools that compute and visualize biomolecular electrostatic surface potential have been used extensively for studying biomolecular function. However, determining the surface potential for large biomolecules on a typical desktop computer can take days or longer using currently available tools and methods. Two commonly used techniques to speed-up these types of electrostatic computations are approximations based on multi-scale coarse-graining and parallelization across multiple processors. This paper demonstrates that for the computation of electrostatic surface potential, these two techniques can be combined to deliver significantly greater speed-up than either one separately, something that is in general not always possible. Specifically, the electrostatic potential computation, using an analytical linearized Poisson-Boltzmann (ALPB) method, is approximated using the hierarchical charge partitioning (HCP) multi-scale method, and parallelized on an ATI Radeon 4870 graphical processing unit (GPU). The implementation delivers a combined 934-fold speed-up for a 476,040 atom viral capsid, compared to an equivalent non-parallel implementation on an Intel E6550 CPU without the approximation. This speed-up is significantly greater than the 42-fold speed-up for the HCP approximation alone or the 182-fold speed-up for the GPU alone.
authors.affiliation: Department of Computer Science, Virginia Tech, 2050 Torgersen Hall 0106, Blacksburg, VA 24061, United States. ramu@cs.vt.edu
authors.forename: Ramu
authors.initials: R
authors.lastname: Anandakrishnan
authors.forename: Tom R W
authors.initials: TR
authors.lastname: Scogland
authors.forename: Andrew T
authors.initials: AT
authors.lastname: Fenley
authors.forename: John C
authors.initials: JC
authors.lastname: Gordon
authors.forename: Wu-chun
authors.initials: WC
authors.lastname: Feng
authors.forename: Alexey V
authors.initials: AV
authors.lastname: Onufriev
mesh_terms: D019295:Computational Biology / Q000295:instrumentation* / Q000379:methods; D003201:Computers; D055672:Static Electricity; D013499:Surface Properties
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