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On using time-averaging restraints in molecular dynamics simulation

Scott, Walter ; Mark, Alan ; van Gunsteren, Wilfred

In: Journal of Biomolecular NMR, 1998, vol. 12, no. 4, p. 501-508

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    Titre
    • On using time-averaging restraints in molecular dynamics simulation
    Auteur
    • Scott, Walter. Laboratory of Physical Chemistry, ETH Zentrum, CH-8092, Zürich, Switzerland
    • Mark, Alan. Laboratory of Physical Chemistry, ETH Zentrum, CH-8092, Zürich, Switzerland
    • van Gunsteren, Wilfred. Laboratory of Physical Chemistry, ETH Zentrum, CH-8092, Zürich, Switzerland
    Type de document
    • Postprint
    Langue
    • Inglese
    Publié dans
    • Journal of Biomolecular NMR, 1998, vol. 12, no. 4, p. 501-508. Kluwer Academic Publishers
    Autre version électronique
    Identifiant OAI-PMH
    • oai:doc.rero.ch:312850
    Summary
    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