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Vibrational subsystem analysis: A method for probing free energies and correlations in the harmonic limit

J. Chem. Phys. 129, 214109 (2008); doi:10.1063/1.3013558

Published 3 December 2008

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H. Lee Woodcock,1 Wenjun Zheng,1 An Ghysels,2 Yihan Shao,3 Jing Kong,3 and Bernard R. Brooks1
1Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
2Center for Molecular Modeling, Ghent University, Proeftuinstraat 86, B-9000 Gent, Belgium
3Q-Chem Inc., The Design Center, Suite 690, 5001 Baum Boulevard, Pittsburgh, Pennsylvania 15213, USA
A new vibrational subsystem analysis (VSA) method is presented for coupling global motion to a local subsystem while including the inertial effects of the environment. The premise of the VSA method is a partitioning of a system into a smaller region of interest and a usually larger part referred to as environment. This method allows the investigation of local-global coupling, a more accurate estimation of vibrational free energy contribution for parts of a large system, and the elimination of the “tip effect” in elastic network model calculations. Additionally, the VSA method can be used as a probe of specific degrees of freedom that may contribute to free energy differences. The VSA approach can be employed in many ways, but it will likely be most useful for estimating activation free energies in QM/MM reaction path calculations. Four examples are presented to demonstrate the utility of this method. ©2008 American Institute of Physics
History: Received 18 June 2008; accepted 13 October 2008; published 3 December 2008
Permalink: http://link.aip.org/link/?JCPSA6/129/214109/1
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KEYWORDS and PACS

Keywords
PACS
  • 33.20.Tp
    Vibrational analysis (molecular spectra)
  • 31.15.V-
    Electron correlation calculations for atoms, ions and molecules
  • YEAR: 2008

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PUBLICATION DATA

ISSN:
0021-9606 (print)   1089-7690 (online)
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