Commun. Comput. Phys., 10 (2011), pp. 1071-1088.


Parallel Molecular Dynamics with Irregular Domain Decomposition

Mauro Bisson 1*, Massimo Bernaschi 2, Simone Melchionna 3

1 Department of Computer Science, University of Rome "Sapienza", Italy.
2 Istituto Applicazioni Calcolo, Consiglio Nazionale delle Ricerche, Rome, Italy.
3 Institute of Material Sciences and Engineering, Ecole Polytechnique Federale de Lausanne, Switzerland; and CNR-IPCF, Istituto Processi Chimico-Fisici, Consiglio Nazionale delle Ricerche, Rome, Italy.

Received 14 August 2010; Accepted (in revised version) 2 December 2010
Available online 7 July 2011
doi:10.4208/cicp.140810.021210a

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.


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PACS: 02.70.Ns
Key words: Molecular dynamics, irregular domain decomposition, parallel algorithms, hemodynamics.

*Corresponding author.
Email: bisson@di.uniroma1.it (M. Bisson), massimo@iac.rm.cnr.it (M. Bernaschi), simone.melchionna@epfl.ch (S. Melchionna)
 

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