Molecular Simulations With The MD-Grape Special-Purpose Computer

  • Martin J. Field
Conference paper
Part of the Astrophysics and Space Science Library book series (ASSL, volume 263)


Fifty years ago computer simulation studies were almost unheard of. Today they are indispensable tools in many areas of human endeavor, notably in science, technology and economics. The causes for this are twofold. First, while a mathematical description or model of a phenomenon is usually possible, the equations arising from such models are often intractable either because they cannot be solved analytically or because the number of variables is too large to be conveniently handled. In these cases the only way to make progress is to resort to approximate or numerical techniques. Second, of course, is the invention, perfection and mass production of the microchip which has brought extraordinary computational power within the reach of even the most miserly research budget. Together these facts have fueled the explosive development of the field of computational science.


Molecular Simulation Quantum Mechanical Method Fast Multipole Method Empirical Force Field Fluctuate Charge Model 
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.
    Allen, M. P. and Tildesley, D. J. (1987) Computer Simulation of Liquids, Oxford University Press, London.Google Scholar
  2. 2.
    Mc Cammon, J. A. and Harvey, S. (1987) Dynamics of Proteins and Nucleic Acids, Cambridge University Press, Cambridge.CrossRefGoogle Scholar
  3. 3.
    Brooks III, C. L., Karplus, M. and Pettitt, B. M. (1988) Proteins: A Theoretical Perspective of Dynamics, Structure and Thermodynamics, Adv. Chem. Phys., 71 1–259.CrossRefGoogle Scholar
  4. 4.
    Davydov, A. S. (1991) Quantum Mechanics, 2nd edit., Pergamon Press, Oxford.Google Scholar
  5. 5.
    Sutcliffe, B. T. (1995) The Idea of a Potential Energy Surface, J. Mol. Struct. (Theochem) 341 217–235.CrossRefGoogle Scholar
  6. 6.
    Szabo, A. and Ostlund, N. S. (1989) Modern Quantum Chemistry: Introduction to Advanced Electronic Structure Theory, Mc Graw-Hill, New York.Google Scholar
  7. 7.
    Hehre, W. J., Radom, L., Schleyer, P. v. R. and Pople, J. A. (1986) Ab Initio Molecular Orbital Theory, J. Wiley and Sons, New York.Google Scholar
  8. 8.
    Parr, R. G. and Yang, W. (1989) Density Functional Theory of Atoms and Molecules, Oxford University Press, Oxford.Google Scholar
  9. 9.
    Burkett, U. and Allinger, N. L. (1982) Molecular Mechanics, Am. Chem. Soc., Washington, D. C..Google Scholar
  10. 10.
    Pople, J. A. and Beveridge, D. L. (1970) Approximate Molecular Orbital Theory, Mc Graw-Hill, New York.Google Scholar
  11. 11.
    See, for example, the articles in Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications, Vol. 2, W. F. van Gunsteren, P. K. Weiner and A. J. Wilkinson (eds.), ESCOM, Leiden (1993).Google Scholar
  12. 12.
    Field, M. J. (1997) Hybrid Quantum Mechanical/Molecular Mechanical Fluctuating Charge Models for Condensed Phase Simulations, Mol. Phys. 91 835–845.CrossRefGoogle Scholar
  13. 13.
    Rappé, A. K. and Goddard, III, W. A. (1991) Charge Equilibration for Molecular Dynamics Simulations, Mol. Phys., 95 3358–3363.Google Scholar
  14. 14.
    Rick, S. W., Stuart, S. J. and Berne, B. J. (1994) Dynamical Fluctuating Charge Force Fields: Application to Liquid Water, J. Chem. Phys., 101 6141–6156.CrossRefGoogle Scholar
  15. 15.
    Fukushige, T., Taiji, M., Makino, J., Ebisuzaki, T. and Sugimoto, D. (1996) A Highly Parallelized Special-Purpose Computer for Many-Body Simulations with an Arbitrary Central Force: MD-GRAPE, Astrophys. J. 468 51–61.CrossRefGoogle Scholar
  16. 16.
    Komeiji, Y., Uebayasi, M., Takata, R., Shimizu, A., Itsukashi, K. and Taiji, M. (1997) Fast and Accurate Molecular Dynamics Simulation of a Protein using a Special-Purpose Computer, J. Comput. Chem. 18 1546–1563.CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2001

Authors and Affiliations

  • Martin J. Field
    • 1
  1. 1.Laboratoire de Dynamique MoléculaireInstitute de Biologie Structurale — Jean-Pierre EbelGrenoble Cedex 1France

Personalised recommendations