Abstract

Electrostatic potential in systems comprised of biological macromolecules and water phase is described by a 2nd order elliptic partial differential equation, known as the Poisson-Boltzmann equation (PBE). DelPhi is a PBE solver (http://compbio.clemson.edu/delphi.php) which adopts finite difference method to solve this equation numerically and has been widely recognized in the biological community due to its efficiency and accuracy. In this work, we introduce an efficient parallel computing technique via the unique implementation of Gauss-Seidel iteration method in DelPhi. The implementation allows for dynamics partitioning of the multiprocessing jobs by decision making algorithm which takes into account the available computing resources associated with a particular computer cluster. Further we demonstrate the advantages of the new parallelized DelPhi by computing the electrostatic potential and the corresponding energies of large supramolecular structures and molecular motors. The work is supported by NIH, NIGMS, grant number 1R01GM093937-01.

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