Volume 10, Issue 4
Parallel Molecular Dynamics with Irregular Domain Decomposition

Mauro Bisson, Massimo Bernaschi & Simone Melchionna

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

Published online: 2011-10

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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.

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@Article{CiCP-10-1071, author = {}, title = {Parallel Molecular Dynamics with Irregular Domain Decomposition}, journal = {Communications in Computational Physics}, year = {2011}, volume = {10}, number = {4}, pages = {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.

}, issn = {1991-7120}, doi = {https://doi.org/10.4208/cicp.140810.021210a}, url = {http://global-sci.org/intro/article_detail/cicp/7475.html} }
TY - JOUR T1 - Parallel Molecular Dynamics with Irregular Domain Decomposition JO - Communications in Computational Physics VL - 4 SP - 1071 EP - 1088 PY - 2011 DA - 2011/10 SN - 10 DO - http://doi.org/10.4208/cicp.140810.021210a UR - https://global-sci.org/intro/article_detail/cicp/7475.html KW - AB -

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.

Mauro Bisson, Massimo Bernaschi & Simone Melchionna. (2020). Parallel Molecular Dynamics with Irregular Domain Decomposition. Communications in Computational Physics. 10 (4). 1071-1088. doi:10.4208/cicp.140810.021210a
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