Journal of Biomolecular NMR

, Volume 12, Issue 4, pp 501–508 | Cite as

On using time-averaging restraints in molecular dynamics simulation

  • Walter R.P. Scott
  • Alan E. Mark
  • Wilfred F. van Gunsteren
Article

Abstract

Introducing experimental values as restraints into molecular dynamics (MD) simulations to bias the values of particular molecular properties, such as nuclear Overhauser effect intensities or distances, 3J coupling constants, chemical shifts or crystallographic structure factors, towards experimental values is a widely used structure refinement method. To account for the averaging of experimentally derived quantities inherent in the experimental techniques, time-averaging restraining methods may be used. In the case of structure refinement using 3J coupling constants from NMR experiments, time-averaging methods previously proposed can suffer from large artificially induced structural fluctuations. A modified time-averaged restraining potential energy function is proposed which overcomes this problem. The different possible approaches are compared using stochastic dynamics simulations of antamanide, a cyclic peptide of ten residues.

computer simulation J-coupling constants molecular dynamics structure refinement time-averaging restraints 

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Copyright information

© Kluwer Academic Publishers 1998

Authors and Affiliations

  • Walter R.P. Scott
    • 1
  • Alan E. Mark
    • 1
  • Wilfred F. van Gunsteren
    • 1
  1. 1.Laboratory of Physical Chemistry, ETH ZentrumZürichSwitzerland

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