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Molecular Dynamics with Constraints

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

Abstract

A method is described to include constraints such as bond lengths and bond angles into molecular dynamics simulations, while retaining cartesian coordinates. The effects of constraints on physical behaviour and computational efficiency are evaluated. A Fortran subroutine (SHAKE) is appended.

Keywords

Bond Angle Bovine Pancreatic Trypsin Inhibitor Verlet Algorithm Angle Constraint Soft Variable 
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.
    J.P. Ryckaert, G. Ciccotti and H.J.C. Berendsen, J. Comput.Phys. 23 (1977) 327.ADSCrossRefGoogle Scholar
  2. 2.
    H. Goldstein, Classical Mechanics, Addison-Wesley, Reading, Mass., 1950.Google Scholar
  3. 3.
    J. Wittenburg, Dynamics of Systems of Rigid Bodies, Teubner, Stuttgart 1977.MATHCrossRefGoogle Scholar
  4. 4.
    M.R. Pear and J.H. Weiner, J.Chem.Phys. 71 (1979) 212.ADSCrossRefGoogle Scholar
  5. 5.
    M. Fixman, J.Chem.Phys. 69 (1978) 1527.ADSCrossRefGoogle Scholar
  6. 6.
    L. Verlet, Phys.Rev. 159 (1967) 98.ADSCrossRefGoogle Scholar
  7. 7.
    J.P. Ryckaert and A. Bellemans, Faraday Discussions Chem.Soc. 66 (1978) 95.CrossRefGoogle Scholar
  8. 8.
    W.F. van Gunsteren, H.J.C. Berendsen and J.A.C. Rullmann, Faraday Discussions Chem. Soc. 66 (1978) 58.Google Scholar
  9. 9.
    W.F. van Gunsteren and H.J.C. Berendsen, Mol.Phys. 34 (1977) 1311.ADSCrossRefGoogle Scholar
  10. 10.
    W.F. van Gunsteren and M. Karplus, “The effect of constraints on the dynamics of macromolecules”, to be published.Google Scholar
  11. 11.
    W.F. van Gunsteren and M. Karplus, J.Comput.Chem. 1 (1980) 266.CrossRefGoogle Scholar
  12. 12.
    J.A. McCammon, B.R. Gelin and M. Karplus, Nature 267 (1977) 585.ADSCrossRefGoogle Scholar
  13. 13.
    N. Go and H.A. Scheraga, Macromolecules 9 (1976) 535.ADSCrossRefGoogle Scholar
  14. 14.
    M. Fixman, Proc.Natl.Acad.Sci. USA 71 (1974) 3050.ADSCrossRefGoogle Scholar
  15. 15.
    E. Helfand, J.Chem.Phys. 71 (1979) 5000.ADSCrossRefGoogle Scholar
  16. 16.
    M. Gottlieb and R.B. Bird, J.Chem.Phys. 65 (1976) 2467.ADSCrossRefGoogle Scholar
  17. 17.
    D. Chandler and B.J. Berne, J.Chem.Phys. 71 (1979) 5386.MathSciNetADSCrossRefGoogle Scholar
  18. 18.
    W.F. van Gunsteren, Mol.Phys. 40 (1980) 1015.ADSCrossRefGoogle Scholar

Copyright information

© Plenum Press, New York 1983

Authors and Affiliations

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

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