The meaning of component analysis: decomposition of the free energy in terms of specific interactions - PubMed (original) (raw)
. 1995 Dec 15;254(5):801-7.
doi: 10.1006/jmbi.1995.0656.
Affiliations
- PMID: 7500351
- DOI: 10.1006/jmbi.1995.0656
The meaning of component analysis: decomposition of the free energy in terms of specific interactions
S Boresch et al. J Mol Biol. 1995.
Abstract
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 for 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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