A simple and easily implemented Monte Carlo algorithm is described which enables configurational-bias sampling of molecules containing branch points and rings with endocyclic and exocyclic atoms. The method overcomes well-known problems associated with sequential configurational-bias sampling methods. A “reservoir” or “library” of fragments are generated with known probability distributions dependent on stiff intramolecular degrees of freedom. Configurational-bias moves assemble the fragments into whole molecules using the energy associated with the remaining degrees of freedom. The methods for generating the fragments are validated on models of propane, isobutane, neopentane, cyclohexane, and methylcyclohexane. It is shown how the sampling method is implemented in the Gibbs ensemble, and validation studies are performed in which the liquid coexistence curves of propane, isobutane, and 2,2-dimethylhexane are computed and shown to agree with accepted values. The method is general and can be used to sample conformational space for molecules of arbitrary complexity in both open and closed statistical mechanical ensembles.
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7 October 2011
Research Article|
October 07 2011
A general and efficient Monte Carlo method for sampling intramolecular degrees of freedom of branched and cyclic molecules
Jindal K. Shah;
Jindal K. Shah
a)
1Department of Chemical and Biomolecular Engineering,
University of Notre Dame
, Notre Dame, Indiana 46556, USA
2The Center for Research Computing,
University of Notre Dame
, Notre Dame, Indiana 46556, USA
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Edward J. Maginn
Edward J. Maginn
1Department of Chemical and Biomolecular Engineering,
University of Notre Dame
, Notre Dame, Indiana 46556, USA
Search for other works by this author on:
a)
Author to whom correspondence should be addressed. Electronic mail: jshah@nd.edu.
J. Chem. Phys. 135, 134121 (2011)
Article history
Received:
July 05 2011
Accepted:
September 11 2011
Citation
Jindal K. Shah, Edward J. Maginn; A general and efficient Monte Carlo method for sampling intramolecular degrees of freedom of branched and cyclic molecules. J. Chem. Phys. 7 October 2011; 135 (13): 134121. https://doi.org/10.1063/1.3644939
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