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On using oscillating time-dependent restraints in MD simulation

Keller, Bettina ; Christen, Markus ; Oostenbrink, Chris ; van Gunsteren, Wilfred

In: Journal of Biomolecular NMR, 2007, vol. 37, no. 1, p. 1-14

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    Title
    • On using oscillating time-dependent restraints in MD simulation
    Author
    • Keller, Bettina. Laboratorium für Physikalische Chemie, ETH Zürich, CH-8093, Zürich, Switzerland
    • Christen, Markus. Laboratorium für Physikalische Chemie, ETH Zürich, CH-8093, Zürich, Switzerland
    • Oostenbrink, Chris. Computational Medicinal Chemistry and Toxicology, Department of Pharmacochemistry, Vrije Universiteit, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
    • van Gunsteren, Wilfred. Laboratorium für Physikalische Chemie, ETH Zürich, CH-8093, Zürich, Switzerland
    Document Type
    • Postprint
    OAI-PMH Identifier
    • oai:doc.rero.ch:316608
    Summary
    The use of time-dependent restraints in molecular simulation in order to generate a conformational ensemble for molecules that is in accordance with measured ensemble averages for particular observable quantities is investigated. Using a model system consisting of liquid butane and the cyclic peptide antamanide the reproduction of particular average 3 J-coupling constant values in a molecular dynamics simulation is analysed. It is shown that the multiple-valuedness and the sizeable gradients of the Karplus curve relating 3 J-coupling constants measured in NMR experiments to the corresponding torsional-angle values cause severe problems when trying to restrain a 3 J-coupling constant to a value close to the extrema of the Karplus curve. The introduction of a factor oscillating with time into the restraining penalty function alleviates this problem and enhances the restrained conformational sampling