About this Journal Submit a Manuscript Table of Contents
Journal of Atomic and Molecular Physics
Volume 2013 (2013), Article ID 579696, 6 pages
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.

Linked References

  1. N. Goga, A. J. Rzepiela, A. H. de Vries, S. J. Marrink, and H. J. C. Berendsen, “Efficient algorithms for Langevin and DPD dynamics,” Journal of Chemical Theory and Computation, vol. 8, no. 10, pp. 3637–3649, 2012. View at Publisher · View at Google Scholar
  2. H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. Dinola, and J. R. Haak, “Molecular dynamics with coupling to an external bath,” The Journal of Chemical Physics, vol. 81, no. 8, pp. 3684–3690, 1984. View at Scopus
  3. Gromacs tool and documentation, http://www.gromacs.org/.
  4. D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark, and H. J. C. Berendsen, “GROMACS: fast, flexible, and free,” Journal of Computational Chemistry, vol. 26, no. 16, pp. 1701–1718, 2005. View at Publisher · View at Google Scholar · View at Scopus
  5. N. Goga, A. J. Rzepiela, M. N. Melo et al., Advances in Planar Lipid Bilayers and Liposomes: (APLBL), vol. 15, Academic Press, Elsevier, 2012.
  6. N. Goga, S. Costache, and S. Marrink, “A multiscalling constant lambda Molecular dynamic Gromacs implementation,” Materiale Plastice, vol. 46, no. 1, pp. 53–57, 2009. View at Scopus
  7. S. A. Moga, N. Goga, and A. Hadar, “Combiningberendsen thermostat with dissipative particle dynamics (DPD) for polymer simulation,” Materiale Plastice, vol. 50, no. 3, 2013.
  8. H. J. C. Berendsen, “Transport properties computed by linear response through weak coupling to a bath,” Computer Simulations in Material Science, vol. 205, pp. 139–155, 1991.
  9. Folding@home, http://folding.stanford.edu.
  10. D. van der Spoel, E. Lindhal, B. Hess, et al., Gromacs user manual version 3. 3., 2006.
  11. J. M. V. A. Koelman and P. J. Hoogerbrugge, “Dynamic simulation of hard sphere suspensions under steady shear,” Europhysics Letters, vol. 21, no. 3, pp. 363–368, 1993.
  12. S. J. Marrink, H. J. Risselada, S. Yefimov, D. P. Tieleman, and A. H. De Vries, “The MARTINI force field: coarse grained model for biomolecular simulations,” Journal of Physical Chemistry B, vol. 111, no. 27, pp. 7812–7824, 2007. View at Publisher · View at Google Scholar · View at Scopus