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1 results

  • Parallel Molecular Dynamics with Irregular Domain Decomposition

  • Mauro Bisson, Massimo Bernaschi, Simone Melchionna
  • Journal:
    Communications in Computational Physics / Volume 10 / Issue 4 / October 2011
    Published online by Cambridge University Press:
    20 August 2015, pp. 1071-1088
    Print publication:
    October 2011

  • 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.