Source:http://linkedlifedata.com/resource/pubmed/id/12666168
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| Predicate | Object |
|---|---|
| rdf:type | |
| lifeskim:mentions | |
| pubmed:issue |
6
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| pubmed:dateCreated |
2003-3-31
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| pubmed:abstractText |
Hybrid energy methods such as QM/MM and ONIOM, that combine different levels of theory into one calculation, have been very successful in describing large systems. Geometry optimization methods can take advantage of the partitioning of these calculations into a region treated at a quantum mechanical (QM) level of theory and the larger, remaining region treated by an inexpensive method such as molecular mechanics (MM). A series of microiterations can be employed to fully optimize the MM region for each optimization step in the QM region. Cartesian coordinates are used for the MM region and are chosen so that the internal coordinates of the QM region remain constant during the microiterations. The coordinates of the MM region are augmented to permit rigid body translation and rotation of the QM region. This is essential if any atoms in the MM region are constrained, but it also improves the efficiency of unconstrained optimizations. Because of the microiterations, special care is needed for the optimization step in the QM region so that the system remains in the same local valley during the course of the optimization. The optimization methodology with microiterations, constraints, and step-size control are illustrated by calculations on bacteriorhodopsin and other systems.
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| pubmed:language |
eng
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| pubmed:journal | |
| pubmed:status |
PubMed-not-MEDLINE
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| pubmed:month |
Apr
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| pubmed:issn |
0192-8651
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| pubmed:author | |
| pubmed:copyrightInfo |
Copyright 2003 Wiley Periodicals, Inc. J Comput Chem 24: 760-769, 2003
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| pubmed:issnType |
Print
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| pubmed:day |
30
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| pubmed:volume |
24
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| pubmed:owner |
NLM
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| pubmed:authorsComplete |
Y
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| pubmed:pagination |
760-9
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| pubmed:year |
2003
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| pubmed:articleTitle |
Geometry optimization with QM/MM, ONIOM, and other combined methods. I. Microiterations and constraints.
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| pubmed:affiliation |
Cherry L. Emerson Center for Scientific Computation, and Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA.
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| pubmed:publicationType |
Journal Article
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