Document Type

Article

Publication Date

6-2013

Publication Title

Journal of Computational Chemistry

Publisher

Wiley

Abstract

Due to the enormous importance of electrostatics in molecular biology, calculating the electrostatic potential and corresponding energies has become a standard computational approach for the study of biomolecules and nano-objects immersed in water and salt phase or other media. However, the electrostatics of large macromolecules and macromolecular complexes, including nano-objects, may not be obtainable via explicit methods and even the standard continuum electrostatics methods may not be applicable due to high computational time and memory requirements. Here, we report further development of the parallelization scheme reported in our previous work (J Comput Chem. 2012 Sep 15; 33(24):1960–6.) to include parallelization of the molecular surface and energy calculations components of the algorithm. The parallelization scheme utilizes different approaches such as space domain parallelization, algorithmic parallelization, multi-threading, and task scheduling, depending on the quantity being calculated. This allows for efficient use of the computing resources of the corresponding computer cluster. The parallelization scheme is implemented in the popular software DelPhi and results in speedup of several folds. As a demonstration of the efficiency and capability of this methodology, the electrostatic potential and electric field distributions are calculated for the bovine mitochondrial supercomplex illustrating their complex topology which cannot be obtained by modeling the supercomplex components alone.

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This manuscript has been published in the Journal of Computational Chemistry. Please find the published version here (note that a subscription is necessary to access this version):

http://onlinelibrary.wiley.com/journal/10.1002/%28ISSN%291096-987X

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