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J Chem Phys. 2013 Mar 7;138(9):094112. doi: 10.1063/1.4793625.

Molecular dynamics simulations with replica-averaged structural restraints generate structural ensembles according to the maximum entropy principle.

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1
Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom.

Erratum in

  • J Chem Phys. 2013 Oct 28;139(16):169903.

Abstract

In order to characterise the dynamics of proteins, a well-established method is to incorporate experimental parameters as replica-averaged structural restraints into molecular dynamics simulations. Here, we justify this approach in the case of interproton distance information provided by nuclear Overhauser effects by showing that it generates ensembles of conformations according to the maximum entropy principle. These results indicate that the use of replica-averaged structural restraints in molecular dynamics simulations, given a force field and a set of experimental data, can provide an accurate approximation of the unknown Boltzmann distribution of a system.

PMID:
23485282
DOI:
10.1063/1.4793625
[Indexed for MEDLINE]

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