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On using oscillating time-dependent restraints in MD simulation

B. Keller, M. Christen, C. Oostenbrink, W. F. van Gunsteren— 2007

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.

TitleOn using oscillating time-dependent restraints in MD simulation
AuthorB. Keller, M. Christen, C. Oostenbrink, W. F. van Gunsteren
Date2007
IdentifierDOI 10.1007/s10858-006-9081-2
Source(s)
CitationJ. Biomol. NMR, 37 (2007), p. 1-14