Jump to main content
Jump to site search

Issue 15, 2008
Previous Article Next Article

A temperature predictor for parallel tempering simulations

Author affiliations

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 http://folding.bmc.uu.se/remd.

Graphical abstract: A temperature predictor for parallel tempering simulations

Back to tab navigation

Publication details

The article was received on 29 Oct 2007, accepted on 30 Jan 2008 and first published on 25 Feb 2008


Article type: Paper
DOI: 10.1039/B716554D
Citation: Phys. Chem. Chem. Phys., 2008,10, 2073-2077
  •   Request permissions

    A temperature predictor for parallel tempering simulations

    A. Patriksson and D. van der Spoel, Phys. Chem. Chem. Phys., 2008, 10, 2073
    DOI: 10.1039/B716554D

Search articles by author

Spotlight

Advertisements