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A temperature predictor for parallel tempering simulations
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. (Van der Spoel)
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. (Van der Spoel)
2008 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 10, no 15, 2073-2077 p.Article in journal (Other (popular science, discussion, etc.)) Published
Abstract [en]

An algorithm is proposed that generates a set of temperatures for use in parallel tempering simulations ( also known as temperature- replica exchange molecular dynamics simulations) of proteins to obtain a desired exchange probability P-des. The input consists of the number of protein atoms and water molecules in the system, information about the use of constraints and virtual sites and the lower temperature limits. The temperatures generated yield probabilities which are very close to Pdes ( correlation 97%), independent of force. field and over a wide temperature range.

Place, publisher, year, edition, pages
2008. Vol. 10, no 15, 2073-2077 p.
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Biochemistry and Molecular Biology
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URN: urn:nbn:se:uu:diva-16715DOI: 10.1039/b716554dISI: 000254634800011OAI: oai:DiVA.org:uu-16715DiVA: diva2:44486
Available from: 2008-06-03 Created: 2008-06-03 Last updated: 2017-12-08Bibliographically approved

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Patriksson, Alexandravan der Spoel, David

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