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Parallel Molecular Dynamics with Irregular Domain Decomposition

Published online by Cambridge University Press:  20 August 2015

Mauro Bisson ,
Massimo Bernaschi  and
Simone Melchionna
Mauro Bisson*
Affiliation:
Department of Computer Science, University of Rome “Sapienza”, Italy
Massimo Bernaschi*
Affiliation:
Istituto Applicazioni Calcolo, Consiglio Nazionale delle Ricerche, Rome, Italy
Simone Melchionna*
Affiliation:
Institute of Material Sciences and Engineering, École Polytechnique Fédérale de Lausanne, Switzerland CNR-IPCF, Istituto Processi Chimico-Fisici, Consiglio Nazionale delle Ricerche, Rome, Italy
*
Corresponding author.Email:[email protected]
Email:[email protected]
Email:[email protected]
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Abstract

The spatial domain of Molecular Dynamics simulations is usually a regular box that can be easily divided in subdomains for parallel processing. Recent efforts aimed at simulating complex biological systems, like the blood flow inside arteries, require the execution of Parallel Molecular Dynamics (PMD) in vessels that have, by nature, an irregular shape. In those cases, the geometry of the domain becomes an additional input parameter that directly influences the outcome of the simulation. In this paper we discuss the problems due to the parallelization of MD in complex geometries and show an efficient and general method to perform MD in irregular domains.

Keywords

02.70.NsMolecular dynamicsirregular domain decompositionparallel algorithmshemodynamics
Type
Research Article
Information
Communications in Computational Physics , Volume 10 , Issue 4 , October 2011 , pp. 1071 - 1088
Copyright
Copyright © Global Science Press Limited 2011

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References

[1]Frenkel, D. and Smit, B., Understanding Molecular Simulation, Academic Press, London, 1996.Google Scholar
[2]Allen, M. P. and Tildesley, D. J., Computer Simulation of Liquids, Clarendon Press, Oxford, 1987.Google Scholar
[3]Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R. D., Kale, L. and Schulten, K., Scalable molecular dynamics with NAMD, J. Comput. Chem., 26 (2005), 1781–1802.Google Scholar
[4]Plimpton, S. J., Fast parallel algorithms for short-range molecular dynamics, J. Comput. Phys., 117 (1995), 1–19.Google Scholar
[5]Harvey, M., Giupponi, G. and De Fabritiis, G., ACEMD: Accelerated molecular dynamics simulations in the microseconds timescale, J. Chem. Theory Comput., 5 (2009), 1632–1639.Google Scholar
[6]Case, D. A.et al., The Amber biomolecular simulation programs, J. Comput. Chem., 26 (2005), 1668–1688.Google Scholar
[7]http://ambermd.org/gpus/.Google Scholar
[8]Mazzeo, M. D. and Coveney, P. V., HemeLB: A high performance parallel lattice-Boltzmann code for large scale fluid flow in complex geometries, Comput. Phys. Commun., 178(12) (2008), 894–914.Google Scholar
[9]Bernaschi, M., Fyta, M., Kaxiras, E., Melchionna, S., Sircar, J. and Succi, S., MUPHY: A parallel MUlti PHYsics/scale code for high performance bio-fluidic simulations, Comput. Phys. Commun., 180 (2009), 1495–1502.CrossRefGoogle Scholar
[10]Melchionna, S., Bernaschi, M., Succi, S., Kaxiras, E., Rybicki, F. J., Mitsouras, D., Coskun, A. U. and Feldman, C. L., Hydrokinetic approach to large-scale cardiovascular blood flow, Comput. Phys. Commun., 181 (2010), 462–472.CrossRefGoogle Scholar
[11]http://glaros.dtc.umn.edu/gkhome/metis/metis/overview.Google Scholar
[12]http://www.labri.fr/perso/pelegrin/scotch/.Google Scholar
[13]http://www.ibm.com/systems/deepcomputing/bluegene/.Google Scholar