On using time-averaging restraints in molecular dynamics simulation

Scott, Walter R. P., Mark, Alan E. and van Gunsteren, W.F. (1998) On using time-averaging restraints in molecular dynamics simulation. Journal of Biomolecular NMR, 12 4: 501-508. doi:10.1023/A:1008306732538


Author Scott, Walter R. P.
Mark, Alan E.
van Gunsteren, W.F.
Title On using time-averaging restraints in molecular dynamics simulation
Journal name Journal of Biomolecular NMR   Check publisher's open access policy
ISSN 0925-2738
1573-5001
Publication date 1998-11
Sub-type Article (original research)
DOI 10.1023/A:1008306732538
Volume 12
Issue 4
Start page 501
End page 508
Total pages 8
Place of publication Dordrecht, Netherlands
Publisher Springer Netherlands
Language eng
Abstract 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.
Keyword Computer simulation
J -coupling constants
Molecular dynamics
Structure refinement
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: School of Chemistry and Molecular Biosciences
 
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Created: Fri, 01 Apr 2011, 11:43:59 EST by Professor Alan Mark on behalf of School of Chemistry & Molecular Biosciences