Path corrected functionals of stochastic trajectories: Towards relative free energy and reaction coordinate calculations

Thomas B. Woolf

doi:10.1016/S0009-2614(98)00427-8

Path corrected functionals of stochastic trajectories: Towards relative free energy and reaction coordinate calculations

Thomas B. Woolf

School of Medicine

Research output: Contribution to journal › Article › peer-review

39 Scopus citations

Abstract

A numerical method for estimating the functional of a stochastic differential equation is evaluated for possible application to biomolecular systems. The approach uses variance reduction for stochastic trajectories to estimate relative free energy differences and define paths between initial and end points. The method shows promise as evidenced by application to simple one and two dimensional trial surfaces. This suggests that the approach may be applicable to more complex biomolecular systems.

Original language	English (US)
Pages (from-to)	433-441
Number of pages	9
Journal	Chemical Physics Letters
Volume	289
Issue number	5-6
DOIs	https://doi.org/10.1016/S0009-2614(98)00427-8
State	Published - Jun 19 1998

ASJC Scopus subject areas

General Physics and Astronomy
Physical and Theoretical Chemistry

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10.1016/S0009-2614(98)00427-8

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title = "Path corrected functionals of stochastic trajectories: Towards relative free energy and reaction coordinate calculations",

abstract = "A numerical method for estimating the functional of a stochastic differential equation is evaluated for possible application to biomolecular systems. The approach uses variance reduction for stochastic trajectories to estimate relative free energy differences and define paths between initial and end points. The method shows promise as evidenced by application to simple one and two dimensional trial surfaces. This suggests that the approach may be applicable to more complex biomolecular systems.",

author = "Woolf, \{Thomas B.\}",

note = "Funding Information: Thanks are given to Alan Grossfield, Jeremy Fennema, Bernard Brooks, and Richard Pastor for valuable discussion. Support from the NIH (R29 GM54782), the Bard Foundation and the Department of Physiology is gratefully acknowledged.",

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AU - Woolf, Thomas B.

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PY - 1998/6/19

Y1 - 1998/6/19

N2 - A numerical method for estimating the functional of a stochastic differential equation is evaluated for possible application to biomolecular systems. The approach uses variance reduction for stochastic trajectories to estimate relative free energy differences and define paths between initial and end points. The method shows promise as evidenced by application to simple one and two dimensional trial surfaces. This suggests that the approach may be applicable to more complex biomolecular systems.

AB - A numerical method for estimating the functional of a stochastic differential equation is evaluated for possible application to biomolecular systems. The approach uses variance reduction for stochastic trajectories to estimate relative free energy differences and define paths between initial and end points. The method shows promise as evidenced by application to simple one and two dimensional trial surfaces. This suggests that the approach may be applicable to more complex biomolecular systems.

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DO - 10.1016/S0009-2614(98)00427-8

M3 - Article

AN - SCOPUS:0032546697

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EP - 441

JO - Chemical Physics Letters

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IS - 5-6

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Path corrected functionals of stochastic trajectories: Towards relative free energy and reaction coordinate calculations

Abstract

ASJC Scopus subject areas

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