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 a

SUBMITTER: Anandakrishnan R 

PROVIDER: S-EPMC2907926 | biostudies-literature | 2010 Jun

REPOSITORIES: biostudies-literature