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Journal of Atomic and Molecular Physics
Volume 2013 (2013), Article ID 579696, 6 pages
http://dx.doi.org/10.1155/2013/579696
Research Article

A Parallelization Scheme for New DPD-B Thermostats

1Faculty of Engineering and Management of Technological Systems (I.M.S.T.), University Politehnica of Bucharest, Splaiul Independenţei 313, 060042 Bucharest, Romania
2Faculty of Engineering in Foreign Languages (F.I.L.S.), University Politehnica of Bucharest, Splaiul Independenţei 313, Room JE 105, 060042 Bucharest, Romania
3Molecular Dynamics Group, Gron Inst Biomolecular Sciences & Biotechnology, Faculty of Mathematics and Natural Sciences, University of Groningen, Nijenborgh 7, 9747 GN Groningen, The Netherlands

Received 28 March 2013; Revised 7 August 2013; Accepted 9 September 2013

Academic Editor: George C. King

Copyright © 2013 S. A. Moga et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

This paper presents the MPI parallelization of a new algorithm—DPD-B thermostat—for molecular dynamics simulations. The presented results are using Martini Coarse Grained Water System. It should be taken into account that molecular dynamics simulations are time consuming. In some cases the running time varies from days to weeks and even months. Therefore, parallelization is one solution for reducing the execution time. The paper describes the new algorithm, the main characteristics of the MPI parallelization of the new algorithm, and the simulation performances.