Year: 2011
Communications in Computational Physics, Vol. 10 (2011), Iss. 4 : pp. 1071–1088
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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Journal Article Details
Publisher Name: Global Science Press
Language: English
DOI: https://doi.org/10.4208/cicp.140810.021210a
Communications in Computational Physics, Vol. 10 (2011), Iss. 4 : pp. 1071–1088
Published online: 2011-01
AMS Subject Headings: Global Science Press
Copyright: COPYRIGHT: © Global Science Press
Pages: 18
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