Repository: Freie Universit├Ąt Berlin, Math Department

On using oscillating time-dependent restraints in MD simulation

Keller, B. and Christen, M. and Oostenbrink, C. and van Gunsteren, W. F. (2007) On using oscillating time-dependent restraints in MD simulation. Journal Of Biomolecular NMR, 37 . pp. 1-14.

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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.

Item Type:Article
Subjects:Physical Sciences > Physics > Mathematical & Theoretical Physics > Computational Physics
Physical Sciences > Chemistry > Physical Chemistry
Biological Sciences > Molecular Biology
ID Code:841
Deposited By: BioComp Admin
Deposited On:12 Mar 2010 11:35
Last Modified:12 Mar 2010 11:36

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