Accelerating Electrostatic Surface Potential Calculation with Multiscale Approximation on Graphics Processing Units

Anandakrishnan, Ramu and Scogland, Tom and Fenley, Andrew T. and Gordon, John and Feng, Wuchun and Onufriev, Alexey (2009) Accelerating Electrostatic Surface Potential Calculation with Multiscale Approximation on Graphics Processing Units . Technical Report TR-09-15, Computer Science, Virginia Tech.

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. This paper demonstrates how one can take advantage of graphic processing units (GPUs) available in today’s typical desktop computer, together with a multiscale approximation method, to significantly speedup such computations. Specifically, the electrostatic potential computation, using an analytical linearized Poisson Boltzmann (ALPB) method, is implemented on an ATI Radeon 4870 GPU in combination with the hierarchical charge partitioning (HCP) multiscale approximation. This implementation delivers a combined 1800-fold speedup for a 476,040 atom viral capsid.