Phys Chem Chem Phys. 2008 Apr 21;10(15):2073-7. Epub 2008 Feb 25.

A temperature predictor for parallel tempering simulations.

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Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, SE-751 24, Uppsala, Sweden.

Abstract

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 Pdes. 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. To facilitate its use, the algorithm has been implemented as a web server at .

PMID:: 18688361; [PubMed - indexed for MEDLINE]

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