DOI: 10.1063/1.472358. The Jacobian factor in free energy simulations

The Jacobian factor in free energy simulations

10.1063/1.472358

Crossref journal-article

AIP Publishing

The Journal of Chemical Physics (317)

Abstract

The role of Jacobian factors in free energy simulations is described. They provide a simple interpretation of ‘‘moment of inertia correction’’ and ‘‘dynamic stretch free energy’’ terms in such simulations. Since the relevant Jacobian factors can often be evaluated analytically by use of the configurational partition function of a polyatomic molecule, it is possible to subtract them from the simulation results when they make unphysical contributions. An important case arises in alchemical simulations that use a single topology method and introduce dummy particles to have the same number of atoms in the initial and final state. The more general utility of the Jacobian factors for simulations of complex systems is briefly discussed.

Bibliography

Boresch, S., & Karplus, M. (1996). The Jacobian factor in free energy simulations. The Journal of Chemical Physics, 105(12), 5145â5154.

Authors 2

Stefan Boresch (first)
Martin Karplus (additional)

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Dates

Type	When
Created	23 years, 1 month ago (July 26, 2002, 8:32 a.m.)
Deposited	1 year, 6 months ago (Feb. 10, 2024, 2:28 p.m.)
Indexed	1 year, 1 month ago (July 11, 2024, 12:40 a.m.)
Issued	28 years, 11 months ago (Sept. 22, 1996)
Published	28 years, 11 months ago (Sept. 22, 1996)
Published Print	28 years, 11 months ago (Sept. 22, 1996)

Funders 0

None

BibTeX

@article{Boresch_1996, title={The Jacobian factor in free energy simulations}, volume={105}, ISSN={1089-7690}, url={http://dx.doi.org/10.1063/1.472358}, DOI={10.1063/1.472358}, number={12}, journal={The Journal of Chemical Physics}, publisher={AIP Publishing}, author={Boresch, Stefan and Karplus, Martin}, year={1996}, month=sep, pages={5145–5154} }

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