| Implementation of umbrella integration within the framework of the empirical valence bond approach. | |
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MedLine Citation:
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PMID: 19319209 Owner: NLM Status: Publisher |
Abstract/OtherAbstract:
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The umbrella integration method for calculating the potential of mean force (PMF) for a chemical reaction is implemented within the empirical valence bond (EVB) framework. In this implementation, the PMF is generated along the energy gap reaction coordinate, and the biasing potential is the difference between the mapping potential, which is defined to be a linear combination of the valence bond state energies, and the EVB ground state energy. The umbrella integration method is based on the derivative of the PMF with respect to the reaction coordinate. An analytical expression for this derivative applicable to certain types of EVB potentials is presented. The advantages of the umbrella integration method are illustrated by the application of both umbrella integration and the weighted histogram analysis method to the hydride transfer reaction catalyzed by the enzyme dihydrofolate reductase. This application demonstrates that the umbrella integration method reduces the statistical errors, converges efficiently, and does not require significantly overlapping windows. A modified version of the weighted histogram analysis method that shares these advantages is also proposed and implemented. |
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Authors:
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Dhruva K Chakravorty; Malika Kumarasiri; Alexander V Soudackov; Sharon Hammes-Schiffer |
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Publication Detail:
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Type: JOURNAL ARTICLE |
Journal Detail:
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Title: Journal of chemical theory and computation Volume: 4 ISSN: 1549-9626 ISO Abbreviation: - Publication Date: 2008 |
Date Detail:
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Created Date: 2009-3-25 Completed Date: - Revised Date: - |
Medline Journal Info:
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Nlm Unique ID: 101232704 Medline TA: J Chem Theory Comput Country: - |
Other Details:
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Languages: ENG Pagination: 1974-1980 Citation Subset: - |
Affiliation:
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Department of Chemistry, 104 Chemistry Building, Pennsylvania State University, University Park, PA 16802; e-mail: shs@chem.psu.edu. |
Export Citation:
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Descriptor/Qualifier:
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| Grant Support | |
ID/Acronym/Agency:
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R01 GM056207-11//NIGMS NIH HHS; R01 GM056207-12//NIGMS NIH HHS |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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