GPU linear and non-linear Poisson–Boltzmann solver module for DelPhi | Zendy

José Colmenares | Zendy; Jesús Ortiz | Zendy; Walter Rocchia | Zendy

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GPU linear and non-linear Poisson–Boltzmann solver module for DelPhi

Author(s) -

José Colmenares,

Jesús Ortiz,

Walter Rocchia

Publication year - 2013

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btt699

Subject(s) - cuda , computer science , solver , speedup , parallel computing , computational science , software , linear system , delphi , linear equation , mathematics , algorithm , programming language , mathematical analysis , geometry

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.

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