Literature DB >> 18688361

A temperature predictor for parallel tempering simulations.

Alexandra Patriksson1, David van der Spoel.   

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 .

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Year:  2008        PMID： 18688361     DOI： 10.1039/b716554d

Source DB:  PubMed          Journal:  Phys Chem Chem Phys        ISSN： 1463-9076            Impact factor:   3.676


  133 in total

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