Equilibrium Molecular Thermodynamics from Kirkwood Sampling
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Publication Date
2015-05-12Journal Title
Journal of Physical Chemistry B
ISSN
1520-6106
Publisher
American Chemical Society
Volume
119
Pages
6155-6169
Language
English
Type
Article
Metadata
Show full item recordCitation
Somani, S., Okamoto, Y., Ballard, A. J., & Wales, D. (2015). Equilibrium Molecular Thermodynamics from Kirkwood Sampling. Journal of Physical Chemistry B, 119 6155-6169. https://doi.org/10.1021/acs.jpcb.5b01800
Abstract
We present two methods for barrierless equilibrium sampling of
molecular systems based on the recently proposed Kirkwood method (J. Chem.
Phys. 2009, 130, 134102). Kirkwood sampling employs low-order correlations
among internal coordinates of a molecule for random (or non-Markovian) sampling
of the high dimensional conformational space. This is a geometrical sampling
method independent of the potential energy surface. The first method is a variant of
biased Monte Carlo, where Kirkwood sampling is used for generating trial Monte
Carlo moves. Using this method, equilibrium distributions corresponding to
different temperatures and potential energy functions can be generated from a given
set of low-order correlations. Since Kirkwood samples are generated independently,
this method is ideally suited for massively parallel distributed computing. The
second approach is a variant of reservoir replica exchange, where Kirkwood
sampling is used to construct a reservoir of conformations, which exchanges
conformations with the replicas performing equilibrium sampling corresponding to
different thermodynamic states. Coupling with the Kirkwood reservoir enhances sampling by facilitating global jumps in the
conformational space. The efficiency of both methods depends on the overlap of the Kirkwood distribution with the target
equilibrium distribution. We present proof-of-concept results for a model nine-atom linear molecule and alanine dipeptide.
Sponsorship
This research was funded by the European Research Council
and EPSRC grant EP/I001352/1. Y.O. was supported, in part,
by the JSPS Grant-in-Aid for Scientific Research on Innovative
Areas (“Dynamical Ordering and Integrated Functions”).
Funder references
EPSRC (EP/I001352/1)
Identifiers
External DOI: https://doi.org/10.1021/acs.jpcb.5b01800
This record's URL: https://www.repository.cam.ac.uk/handle/1810/250404
Rights
Attribution 2.0 UK: England & Wales
Licence URL: http://creativecommons.org/licenses/by/2.0/uk/
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