TY - JOUR
T1 - Parallel Molecular Dynamics with Irregular Domain Decomposition
AU - Mauro Bisson, Massimo Bernaschi & Simone Melchionna
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 - <p style="text-align: justify;">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.</p>