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Stochastic Dynamics of Polymers

  • W. F. van Gunsteren
  • H. J. C. Berendsen
Part of the NATO Advanced Science Institutes Series book series (volume 92)

Abstract

When simulating a molecular system by the method of stochastic dynamics (SD), less interesting degrees of freedom are ignored and their influence on the other degrees of freedom is approximated by a combination of mean force interactions, stochastic forces and frictional forces. When time and space correlations in the latter are neglected, SD reduces to its simplest form, Brownian dynamics (BD). A BD algorithm is derived and applied to liquid n-butane and n-decane, where one molecule is considered explicitly and the surrounding liquid is modelled stochastically. From a comparison of the results to those of molecular dynamics (MD) simulations of these liquids it is concluded that the BD model yields a good approximation of the dynamics of n-alkanes in the liquid state.

Keywords

Molecular Dynamic Molecular Dynamic Simulation Hydrodynamic Interaction Stochastic Force Space Correlation 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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References

  1. 1.
    D.J. Adams, Chem. Phys. Letters 62 (1979) 329.ADSCrossRefGoogle Scholar
  2. 2.
    J.A. McCammon, B.R. Gelin and M. Karplus, Nature 267 (1977) 585.ADSCrossRefGoogle Scholar
  3. 3.
    L.R. Pratt and D. Chandler, J.Chem.Phys. 67 (1977) 3683.ADSCrossRefGoogle Scholar
  4. 4.
    F.M. Richards, Ann.Rev.Biophys.Bioeng. 6 (1977) 151.CrossRefGoogle Scholar
  5. 5.
    P. Turq, F. Lantelme and H.L. Friedman, J.Chem.Phys. 66 (1977) 3039.ADSCrossRefGoogle Scholar
  6. 6.
    R. Kubo, Rep.Prog.Phys. 29 (1966) 255.ADSCrossRefGoogle Scholar
  7. 7.
    W.F. van Gunsteren, H.J.C. Berendsen and J.A.C. Rullmann, “Stochastic Dynamics for Molecules with Constraints, Brownian Dynamics of n-alkanes”, submitted to Mol.Phys.Google Scholar
  8. 8.
    J.D. Doll and D.R. Dion, J.Chem.Phys. 65 (1976) 3762.ADSCrossRefGoogle Scholar
  9. 9.
    G. Cicotti and J.P. Ryckaert, Mol.Phys. 40 (1980) 141.ADSCrossRefGoogle Scholar
  10. 10.
    S.A. Adelman, J.Chem.Phys. 71 (1979) 4471.ADSCrossRefGoogle Scholar
  11. 11.
    D.L. Ermak and J.A. McCammon, J.Chem.Phys. 69 (1978) 1352.ADSCrossRefGoogle Scholar
  12. 12.
    J.S. McCaskill and R.G. Gilberg, Chem.Phys. 44 (1979) 389.CrossRefGoogle Scholar
  13. 13.
    J.P. Ryckaert, “Simulation de n-alkanes liquides par la méthode de dynamique moléculaire”, thesis, Université Libre de Bruxelles, Brussels, 1976.Google Scholar
  14. 14.
    J.P. Ryckaert and A. Bellemans, Faraday Disc.Chem.Soc. 66 (1978) 95.CrossRefGoogle Scholar
  15. 15.
    W.F. van Gunsteren and H.J.C. Berendsen, “Algorithms for Brownian Dynamics”, to be published.Google Scholar
  16. 16.
    D.L. Ermak and H. Buckholtz, “Numerical Integration of the Langevin Equation: Monte Carlo Simulation”, preprint, 1978.Google Scholar
  17. 17.
    L. Verlet, Phys.Rev. 159 (1967) 98.ADSCrossRefGoogle Scholar
  18. 18.
    W.F. van Gunsteren and H.J.C. Berendsen, Mol.Phys. 34 (1977) 1311.ADSCrossRefGoogle Scholar
  19. 19.
    A. Papoulis, “Probability, Random Variables, and Stochastic Processes, McGraw-Hill, 1965.MATHGoogle Scholar
  20. 20.
    J.P. Ryckaert, G. Ciccotti and H.J.C. Berendsen, J.Comput.Phys. 23 (1977) 327.ADSCrossRefGoogle Scholar
  21. 21.
    D. Chandler, Faraday Disc.Chem.Soc. 66 (1978) 184.CrossRefGoogle Scholar
  22. 22.
    R.M. Levy, M. Karplus and J.A. McCammon, Chem.Phys.Letters 65 (1979) 4.ADSCrossRefGoogle Scholar
  23. 23.
    D. Beece et al., “Solvent Viscosity and Protein Dynamics”, Biochemistry (1980) in press.Google Scholar

Copyright information

© Plenum Press, New York 1983

Authors and Affiliations

  • W. F. van Gunsteren
    • 1
  • H. J. C. Berendsen
    • 1
  1. 1.Laboratory of Physical ChemistryUniversity of GroningenGroningenThe Netherlands

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