DOI: 10.1063/1.2174010. On the use of transition matrix methods with extended ensembles

On the use of transition matrix methods with extended ensembles

10.1063/1.2174010

Crossref journal-article

AIP Publishing

The Journal of Chemical Physics (317)

Abstract

Different extended ensemble schemes for non-Boltzmann sampling (NBS) of a selected reaction coordinate λ were formulated so that they employ (i) “variable” sampling window schemes (that include the “successive umbrella sampling” method) to comprehensibly explore the λ domain and (ii) transition matrix methods to iteratively obtain the underlying free-energy η landscape (or “importance” weights) associated with λ. The connection between “acceptance ratio” and transition matrix methods was first established to form the basis of the approach for estimating η(λ). The validity and performance of the different NBS schemes were then assessed using as λ coordinate the configurational energy of the Lennard-Jones fluid. For the cases studied, it was found that the convergence rate in the estimation of η is little affected by the use of data from high-order transitions, while it is noticeably improved by the use of a broader window of sampling in the variable window methods. Finally, it is shown how an “elastic” window of sampling can be used to effectively enact (nonuniform) preferential sampling over the λ domain, and how to stitch the weights from separate one-dimensional NBS runs to produce a η surface over a two-dimensional domain.

Bibliography

Escobedo, F. A., & Abreu, C. R. A. (2006). On the use of transition matrix methods with extended ensembles. The Journal of Chemical Physics, 124(10).

Authors 2

Fernando A. Escobedo (first)
Charlles R. A. Abreu (additional)

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Dates

Type	When
Created	19 years, 5 months ago (March 9, 2006, 6:02 p.m.)
Deposited	2 years, 2 months ago (June 26, 2023, 1:39 a.m.)
Indexed	1 month, 1 week ago (July 30, 2025, 6:46 a.m.)
Issued	19 years, 5 months ago (March 13, 2006)
Published	19 years, 5 months ago (March 13, 2006)
Published Online	19 years, 5 months ago (March 13, 2006)
Published Print	19 years, 5 months ago (March 14, 2006)

Funders 0

None

BibTeX

@article{Escobedo_2006, title={On the use of transition matrix methods with extended ensembles}, volume={124}, ISSN={1089-7690}, url={http://dx.doi.org/10.1063/1.2174010}, DOI={10.1063/1.2174010}, number={10}, journal={The Journal of Chemical Physics}, publisher={AIP Publishing}, author={Escobedo, Fernando A. and Abreu, Charlles R. A.}, year={2006}, month=mar }

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