Parallel Molecular Dynamics with Irregular Domain Decomposition

The spatial domain of Molecular Dynamics simulations is usually a regular box that 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.


Published in:
Communications In Computational Physics, 10, 1071-1088
Year:
2011
Keywords:
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 Record created 2012-06-25, last modified 2018-09-13


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