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 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 P_des (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.