Continuous development of schemes for parallel computing of the electrostatics in biological systems: Implementation in DelPhi
Article first published online: 3 JUN 2013
Copyright © 2013 Wiley Periodicals, Inc.
Journal of Computational Chemistry
Volume 34, Issue 22, pages 1949–1960, 15 August 2013
How to Cite
How to cite this article: J. Comput. Chem. 2013, 34, 1949–1960. DOI: 10.1002/jcc.23340, , , ,
- Issue published online: 8 JUL 2013
- Article first published online: 3 JUN 2013
- Manuscript Accepted: 2 MAY 2013
- Manuscript Revised: 3 APR 2013
- Manuscript Received: 19 FEB 2013
- National Institute of General Medical Sciences, National Institutes of Health. Grant Number: R01 GM093937
- Poisson-Boltzmann equation;
- parallel computing
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 (Li, et al., J. Comput. Chem. 2012, 33, 1960) 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, multithreading, 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. © 2013 Wiley Periodicals, Inc.