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J Chem Phys. 2013 Feb 28;138(8):084107. doi: 10.1063/1.4792208.

On the statistical equivalence of restrained-ensemble simulations with the maximum entropy method.

Author information

1
Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago, Chicago, Illinois 60637, USA. roux@uchicago.edu

Abstract

An issue of general interest in computer simulations is to incorporate information from experiments into a structural model. An important caveat in pursuing this goal is to avoid corrupting the resulting model with spurious and arbitrary biases. While the problem of biasing thermodynamic ensembles can be formulated rigorously using the maximum entropy method introduced by Jaynes, the approach can be cumbersome in practical applications with the need to determine multiple unknown coefficients iteratively. A popular alternative strategy to incorporate the information from experiments is to rely on restrained-ensemble molecular dynamics simulations. However, the fundamental validity of this computational strategy remains in question. Here, it is demonstrated that the statistical distribution produced by restrained-ensemble simulations is formally consistent with the maximum entropy method of Jaynes. This clarifies the underlying conditions under which restrained-ensemble simulations will yield results that are consistent with the maximum entropy method.

PMID:
23464140
PMCID:
PMC3598863
DOI:
10.1063/1.4792208
[Indexed for MEDLINE]
Free PMC Article

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