title: On using oscillating time-dependent restraints in MD simulation.
abstract: 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.
authors.affiliation: Laboratorium für Physikalische Chemie, ETH Zürich, Zürich, CH-8093, Switzerland.
authors.forename: Bettina
authors.initials: B
authors.lastname: Keller
authors.forename: Markus
authors.initials: M
authors.lastname: Christen
authors.forename: Chris
authors.initials: C
authors.lastname: Oostenbrink
authors.forename: Wilfred F
authors.initials: WF
authors.lastname: van Gunsteren
mesh_terms: D000465:Algorithms; D002073:Butanes / Q000737:chemistry; D003198:Computer Simulation; D008956:Models, Chemical; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D010456:Peptides, Cyclic / Q000737:chemistry
chemical_list: D002073:Butanes; D010456:Peptides, Cyclic; C100265:antamanide; C046888:butane