The Meaning of Component Analysis: Decomposition of the Free Energy in Terms of Specific Interactions

Free energy simulations are of particular interest for the interpretation of macroscopic data in terms of microscopic interactions. This can be done by expressing calculated free energies as a sum of components that correspond to the contributions of different energy terms or different parts of the...

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Published in:Journal of molecular biology 1995-12, Vol.254 (5), p.801-807
Main Authors: Boresch, S., Karplus, M.
Format: Article
Language:English
Subjects:
alchemical simulations
Alchemy
component analysis
Computer Simulation
Energy Transfer
free energy decomposition
Models, Theoretical
mutant analysis
thermodynamics
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creator Boresch, S.
Karplus, M.
description Free energy simulations are of particular interest for the interpretation of macroscopic data in terms of microscopic interactions. This can be done by expressing calculated free energies as a sum of components that correspond to the contributions of different energy terms or different parts of the system. Since the resulting components depend on the integration path, care is required in their use. We show that a linear coupling scheme for the alchemical creation of a chemical identity corresponds to a particularly useful path because it leads to a symmetric decoupling of the free energy components. The path dependence also provides an additional degree of freedom that can be used to study different processes. This latter point is illustrated by a reinterpretation of a recent simulation on wild-type and mutant azurin by Mark and van Gunsteren.
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subjects alchemical simulations
Alchemy
component analysis
Computer Simulation
Energy Transfer
free energy decomposition
Models, Theoretical
mutant analysis
thermodynamics
title The Meaning of Component Analysis: Decomposition of the Free Energy in Terms of Specific Interactions
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