title: A temperature predictor for parallel tempering simulations.
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 .
authors.affiliation: Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, SE-751 24, Uppsala, Sweden.
authors.forename: Alexandra
authors.initials: A
authors.lastname: Patriksson
authors.forename: David
authors.initials: D
authors.lastname: van der Spoel
mesh_terms: D003198:Computer Simulation; D008954:Models, Biological; D011506:Proteins / Q000737:chemistry; D013696:Temperature; D014867:Water / Q000737:chemistry
chemical_list: D011506:Proteins; D014867:Water