This site contains a webserver for generating temperatures for REMD-calculations. You submit the number of protein atoms and water molecules in your system, and an upper and lower limit for the temperature range, information about constraints and/or virtual sites and a desired exchange probability Pdes, and the webserver will predict a temperature series with correspondig energy differences and standard deviations which matches the desired probability Pdes. You can then use these temperatures in REMD simulations.
A word of caution is in place here. The derivation of the parameters for the prediction was done with the OPLS/AA force field and the GROMACS software. When using other force fields, software and/or other algorithms (cut-off treatment, pressure and temperature scaling etc.) results may deviate, although the tests performed in our paper, including using the GROMOS96 force field, show that these deviations are minor. Nevertheless you are encouraged to check your exchange probabilities, and compare them to the desired probabilities.
If you use the results from this webserver in simulations which are published in scientific journals, please
Alexandra Patriksson and David van der Spoel, A temperature predictor for parallel tempering simulations Phys. Chem. Chem. Phys., 10 pp. 2073-2077 (2008) http://dx.doi.org/10.1039/b716554d.
We also recommend the following literature about theory behind replica exchange simulations [1,2] and applications of REMD [3,4]. A recent review about sampling is in ref. .
In case of questions please mail to t-remd at xray.bmc.uu.se.