The European Physical Journal Special Topics

, Volume 200, Issue 1, pp 211–223 | Cite as

SHAKE parallelization

  • R. Elber
  • A. P. Ruymgaart
  • B. Hess


SHAKE is a widely used algorithm to impose general holonomic constraints during molecular simulations. By imposing constraints on stiff degrees of freedom that require integration with small time steps (without the constraints) we are able to calculate trajectories with time steps larger by approximately a factor of two. The larger time step makes it possible to run longer simulations. Another approach to extend the scope of Molecular Dynamics is parallelization. Parallelization speeds up the calculation of the forces between the atoms and makes it possible to compute longer trajectories with better statistics for thermodynamic and kinetic averages. A combination of SHAKE and parallelism is therefore highly desired. Unfortunately, the most widely used SHAKE algorithm (of bond relaxation) is inappropriate for parallelization and alternatives are needed. The alternatives must minimize communication, lead to good load balancing, and offer significantly better performance than the bond relaxation approach. The algorithm should also scale with the number of processors. We describe the theory behind different implementations of constrained dynamics on parallel systems, and their implementation on common architectures.


Molecular Dynamics Lagrange Multiplier European Physical Journal Special Topic Molecular Simulation Small Time Step 
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.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    J.P. Ryckaert, G. Ciccotti, H.J.C. Berendsen, J. Comput. Phys. 23, 327 (1977)CrossRefADSGoogle Scholar
  2. 2.
    E. Barth, et al., J. Comput. Chem. 16, 1192 (1995)CrossRefGoogle Scholar
  3. 3.
    Y. Weinbach, R. Elber, J. Comput. Phys. 209, 193 (2005)CrossRefzbMATHADSMathSciNetGoogle Scholar
  4. 4.
    B. Hess, et al., J. Comput. Chem. 18, 1463 (1997)CrossRefGoogle Scholar
  5. 5.
    B. Hess, J. Chemical Theory, Computation 4, 116 (2008)CrossRefGoogle Scholar
  6. 6.
    A.G. Bailey, C.P. Lowe, J. Comput. Chem. 30, 2485 (2009)CrossRefGoogle Scholar
  7. 7.
    A.G. Bailey, C.P. Lowe, A.P. Sutton, J. Comput. Phys. 227, 8949 (2008)CrossRefzbMATHADSMathSciNetGoogle Scholar
  8. 8.
    P. Gonnet, J. Comput. Phys. 220, 740 (2007)CrossRefzbMATHADSMathSciNetGoogle Scholar
  9. 9.
    H.C. Andersen, J. Comput. Phys. 52, 24 (1983)CrossRefzbMATHADSGoogle Scholar
  10. 10.
    M.J. Harvey, G. Giupponi, G. De Fabritiis, J. Chem. Theory Comput. 5, 1632 (2009)CrossRefGoogle Scholar
  11. 11.
    J.E. Stone, et al., J. Comput. Chem. 28, 2618 (2007)CrossRefGoogle Scholar
  12. 12.
    R. Elber, et al., Comp. Phys. Commun. 91, 159 (1995)CrossRefADSGoogle Scholar
  13. 13.
    K.J. Bowers, et al., Scientific Computing (Tampa, Florida: IEEE, 2006)Google Scholar
  14. 14.
    S.E. Debolt, Kollman P.A., J. Comput. Chem. 14, 312 (1993)CrossRefGoogle Scholar
  15. 15.
    J.E. Mertz, et al., J. Comput. Chem. 12, 1270 (1991)CrossRefGoogle Scholar
  16. 16.
    R. Fletcher, Practical methods of optimization (John Wiley & Sons, 2000), p. 436Google Scholar
  17. 17.
    J. Nocedal, S.J. Wright, Numerical Optimization. Springer Series in Operation Research, edited by P. Glynn, S.M. Robinson (Springer, New York, 1999)Google Scholar
  18. 18.
    P. Eastman, V.S. Pander, J. Chem. Theory and Comput. 6, 434 (2010)CrossRefGoogle Scholar
  19. 19.
    T. Noguti, N. Go, Proteins-Structure Function and Genetics 5, 104 (1989)CrossRefGoogle Scholar

Copyright information

© EDP Sciences and Springer 2011

Authors and Affiliations

  • R. Elber
    • 1
  • A. P. Ruymgaart
    • 1
  • B. Hess
    • 2
  1. 1.Institute for Computational Engineering and Sciences, Department of Chemistry and BiochemistryUniversity of Texas at AustinAustinUSA
  2. 2.KTH Royal Institute of Technology, Department of Theoretical PhysicsAlbanova University CenterStockholmSweden

Personalised recommendations