Source:http://linkedlifedata.com/resource/pubmed/id/16090139
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| Predicate | Object |
|---|---|
| rdf:type | |
| lifeskim:mentions | |
| pubmed:issue |
1 Pt 2
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| pubmed:dateCreated |
2005-8-10
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| pubmed:abstractText |
The rugged Metropolis (RM) algorithm is a biased updating scheme which aims at directly hitting the most likely configurations in a rugged free-energy landscape. Details of the one-variable ( RM1 ) implementation of this algorithm are presented. This is followed by an extension to simultaneous updating of two dynamical variables ( RM2 ). In a test with the brain peptide Met-Enkephalin in vacuum RM2 improves conventional Metropolis simulations by a factor of about 4. Correlations between three or more dihedral angles appear to prevent larger improvements at low temperatures. We also investigate a multihit Metropolis scheme, which spends more CPU time on variables with large autocorrelation times.
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| pubmed:grant | |
| pubmed:language |
eng
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| pubmed:journal | |
| pubmed:citationSubset |
IM
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| pubmed:chemical | |
| pubmed:status |
MEDLINE
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| pubmed:month |
Jul
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| pubmed:issn |
1539-3755
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| pubmed:author | |
| pubmed:issnType |
Print
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| pubmed:volume |
72
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| pubmed:owner |
NLM
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| pubmed:authorsComplete |
Y
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| pubmed:pagination |
016712
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| pubmed:dateRevised |
2007-11-14
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| pubmed:meshHeading |
pubmed-meshheading:16090139-Algorithms,
pubmed-meshheading:16090139-Animals,
pubmed-meshheading:16090139-Biophysics,
pubmed-meshheading:16090139-Brain,
pubmed-meshheading:16090139-Computer Simulation,
pubmed-meshheading:16090139-Computers,
pubmed-meshheading:16090139-Enkephalin, Methionine,
pubmed-meshheading:16090139-Humans,
pubmed-meshheading:16090139-Models, Chemical,
pubmed-meshheading:16090139-Models, Statistical,
pubmed-meshheading:16090139-Models, Theoretical,
pubmed-meshheading:16090139-Molecular Conformation,
pubmed-meshheading:16090139-Monte Carlo Method,
pubmed-meshheading:16090139-Peptides,
pubmed-meshheading:16090139-Protein Conformation,
pubmed-meshheading:16090139-Protein Folding,
pubmed-meshheading:16090139-Temperature,
pubmed-meshheading:16090139-Thermodynamics,
pubmed-meshheading:16090139-Time Factors
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| pubmed:year |
2005
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| pubmed:articleTitle |
Rugged Metropolis sampling with simultaneous updating of two dynamical variables.
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| pubmed:affiliation |
Department of Physics, Florida State University, Tallahassee, Florida 32306-4350, USA.
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| pubmed:publicationType |
Journal Article,
Research Support, U.S. Gov't, P.H.S.,
Research Support, N.I.H., Extramural
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