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Sampling conformations in high dimensions using low-dimensional distribution functions

J. Chem. Phys. 130, 134102 (2009); doi:10.1063/1.3088434

Published 2 April 2009

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Sandeep Somani, Benjamin J. Killian, and Michael K. Gilson
Center for Advanced Research in Biotechnology, UMBI, 9600 Gudelsky Drive, Rockville, Maryland 20850, USA
We present an approximation to a molecule's N-dimensional conformational probability density function (pdf) in terms of marginal pdfs of highest order l, where l is much less than N. The approximation is constructed as a product of conditional pdfs derived by recursive application of the generalized Kirkwood superposition approximation. Furthermore, an algorithm is presented to sample conformations from the approximate full-dimensional pdf based upon all input marginal pdfs. The sampling algorithm is tested for three small molecule systems by using the algorithm to sample conformations at levels l=1, 2, or 3 and comparing the distributions of sampled conformations with those from the molecular dynamics (MD) simulations. The distributions of conformations sampled at third (l=3) order resemble the MD distributions rather well and significantly better than those sampled at second (l=2) or first (l=1) order. In addition to highlighting the importance of correlations among internal degrees of freedom, these results suggest that low-order correlations suffice to describe most of the conformational fluctuations of molecules in a thermal environment. ©2009 American Institute of Physics
History: Received 5 September 2008; accepted 4 February 2009; published 2 April 2009
Permalink: http://link.aip.org/link/?JCPSA6/130/134102/1
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KEYWORDS and PACS

Keywords
PACS
  • 33.15.Bh
    General molecular conformation and symmetry; stereochemistry
  • 31.15.-p
    Calculations and mathematical techniques in atomic and molecular physics
  • YEAR: 2009

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