title: GPU linear and non-linear Poisson-Boltzmann solver module for DelPhi.
abstract: CONCLUSIONS
  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.
  
  
  METHODS
  The module is open-source and available at http://www.electrostaticszone.eu/index.php/downloads.
authors.affiliation: Drug Discovery and Development Department and Advanced Robotics Department, Istituto Italiano di Tecnologia (IIT), via Morego, 30, 16163 Genova - Italy.
authors.forename: José
authors.initials: J
authors.lastname: Colmenares
authors.forename: Jesús
authors.initials: J
authors.lastname: Ortiz
authors.forename: Walter
authors.initials: W
authors.lastname: Rocchia
mesh_terms: D000465:Algorithms; D000581:Amidohydrolases / Q000737:chemistry*; D019295:Computational Biology / Q000379:methods*; D006801:Humans; D017711:Nonlinear Dynamics; D012984:Software; D055672:Static Electricity; D000099252:Fatty Acid Amide Hydrolases
chemical_list: D000581:Amidohydrolases; D000099252:Fatty Acid Amide Hydrolases