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MBO(N)D: A multibody method for long-time molecular dynamics simulations

  1. Hon M. Chun1,*,
  2. Carlos E. Padilla1,
  3. Donovan N. Chin1,
  4. Masakatsu Watanabe1,
  5. Valeri I. Karlov1,
  6. Howard E. Alper1,
  7. Keto Soosaar1,
  8. Kim B. Blair1,
  9. Oren M. Becker2,
  10. Leo S. D. Caves3,
  11. Robert Nagle4,
  12. David N. Haney5,
  13. Barry L. Farmer6

Article first published online: 28 JAN 2000

DOI: 10.1002/(SICI)1096-987X(200002)21:3<159::AID-JCC1>3.0.CO;2-J

Issue

Journal of Computational Chemistry

Journal of Computational Chemistry

Volume 21, Issue 3, pages 159–184, February 2000

Additional Information

How to Cite

Chun, H. M., Padilla, C. E., Chin, D. N., Watanabe, M., Karlov, V. I., Alper, H. E., Soosaar, K., Blair, K. B., Becker, O. M., Caves, L. S. D., Nagle, R., Haney, D. N. and Farmer, B. L. (2000), MBO(N)D: A multibody method for long-time molecular dynamics simulations. J. Comput. Chem., 21: 159–184. doi: 10.1002/(SICI)1096-987X(200002)21:3<159::AID-JCC1>3.0.CO;2-J

Author Information

  1. 1

    Moldyn, Inc., 955 Massachusetts Avenue, Cambridge, Massachusetts 02139

  2. 2

    School of Chemistry, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel

  3. 3

    Protein Structure Research Group, University of York, York YO15DD, United Kingdom

  4. 4

    Department of Chemistry, Harvard University, Cambridge, Massachusetts 02138

  5. 5

    Haney Associates, Inc., 5455 Westknoll Drive, La Jolla, California 92037

  6. 6

    Air Force Research Laboratory, Wright–Patterson Air Force Base, Ohio 45433

*Moldyn, Inc., 955 Massachusetts Avenue, Cambridge, Massachusetts 02139

Publication History

  1. Issue published online: 28 JAN 2000
  2. Article first published online: 28 JAN 2000
  3. Manuscript Accepted: 14 SEP 1999
  4. Manuscript Received: 24 NOV 1998

Funded by

  • Advanced Technology Program. Grant Number: 70NANB5H1078
  • National Science Foundation. Grant Number: 9361843
  • National Cancer Institute. Grant Number: CA60211-03
  • Photon Research Associates, Inc.

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Keywords:

  • molecular dynamics;
  • normal modes;
  • anharmonicity;
  • macromolecules;
  • numerical integrators

Abstract

A modeling approach that can significantly speed up the dynamics simulation of large molecular systems is presented herein. A multigranular modeling approach, whereby different parts of the molecule are modeled at different levels of detail, is enabled by substructuring. Substructuring the molecular system is accomplished by collecting groups of atoms into rigid or flexible bodies. Body flexibility is modeled by a truncated set of body-based modes. This approach allows for the elimination of the high-frequency harmonic motion while capturing the low-frequency anharmonic motion of interest. This results in the use of larger integration step sizes, substantially reducing the computational time required for a given dynamic simulation. The method also includes the use of a multiple time scale (MTS) integration scheme. Speed increases of 5- to 30-fold over atomistic simulations have been realized in various applications of the method. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 159–184, 2000

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