José Colmenares1, Jesús Ortiz, Walter Rocchia. 1. Drug Discovery and Development Department and Advanced Robotics Department, Istituto Italiano di Tecnologia (IIT), via Morego, 30, 16163 Genova - Italy.
Abstract
SUMMARY: In this work, we present a CUDA-based GPU implementation of a Poisson-Boltzmann equation solver, in both the linear and non-linear versions, using double precision. A finite difference scheme is adopted and made suitable for the GPU architecture. The resulting code was interfaced with the electrostatics software for biomolecules DelPhi, which is widely used in the computational biology community. The algorithm has been implemented using CUDA and tested over a few representative cases of biological interest. Details of the implementation and performance test results are illustrated. A speedup of ~10 times was achieved both in the linear and non-linear cases. AVAILABILITY AND IMPLEMENTATION: The module is open-source and available at http://www.electrostaticszone.eu/index.php/downloads.
SUMMARY: In this work, we present a CUDA-based GPU implementation of a Poisson-Boltzmann equation solver, in both the linear and non-linear versions, using double precision. A finite difference scheme is adopted and made suitable for the GPU architecture. The resulting code was interfaced with the electrostatics software for biomolecules DelPhi, which is widely used in the computational biology community. The algorithm has been implemented using CUDA and tested over a few representative cases of biological interest. Details of the implementation and performance test results are illustrated. A speedup of ~10 times was achieved both in the linear and non-linear cases. AVAILABILITY AND IMPLEMENTATION: The module is open-source and available at http://www.electrostaticszone.eu/index.php/downloads.
Authors: José Colmenares; Antonella Galizia; Jesús Ortiz; Andrea Clematis; Walter Rocchia Journal: Biomed Res Int Date: 2014-06-12 Impact factor: 3.411