Optimized parallel tempering simulations of proteins

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dc.creatorTrebst, Simon
dc.creatorTroyer, Matthias
dc.creatorHansmann, Ulrich H. E.
dc.date2006-02-06
dc.date.accessioned2026-07-07T07:04:11Z
dc.date.available2026-07-07T07:04:11Z
dc.descriptionWe apply a recently developed adaptive algorithm that systematically improves the efficiency of parallel tempering or replica exchange methods in the numerical simulation of small proteins. Feedback iterations allow us to identify an optimal set of temperatures/replicas which are found to concentrate at the bottlenecks of the simulations. A measure of convergence for the equilibration of the parallel tempering algorithm is discussed. We test our algorithm by simulating the 36-residue villin headpiece sub-domain HP-36 wherewe find a lowest-energy configuration with a root-mean-square-deviation of less than 4 Angstroem to the experimentally determined structure.
dc.description22 pages, 7 figures
dc.identifierhttps://arxiv.org/abs/q-bio/0602005
dc.identifierhttp://arxiv.org/abs/q-bio/0602005
dc.identifierJ. Chem. Phys. 124, 174903 (2006).
dc.identifierdoi:10.1063/1.2186639
dc.identifier.urihttp://salesiana.dossiersoluciones.com/handle/123456789/109267
dc.subjectQuantitative Methods
dc.subjectStatistical Mechanics
dc.subjectComputational Physics
dc.titleOptimized parallel tempering simulations of proteins
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