GPU linear and non-linear Poisson-Boltzmann solver module for DelPhi.
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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.
SUBMITTER: Colmenares J
PROVIDER: S-EPMC3928518 | biostudies-literature | 2014 Feb
REPOSITORIES: biostudies-literature
Publications
GPU linear and non-linear Poisson-Boltzmann solver module for DelPhi.
Colmenares José J Ortiz Jesús J Rocchia Walter W
Bioinformatics (Oxford, England) 20131130 4
<h4>Summary</h4>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 c ...[more]
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