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 P_{des}, and the webserver
will predict a temperature series with correspondig energy differences
and standard deviations which matches the desired probability
P_{des}. You can then use these temperatures in REMD
simulations.

The code for this webserver can be downloaded from github at https://github.com/dspoel/remd.

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
cite:

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. [5].

- K. Hukushima and K. Nemoto:
*Exchange Monte Carlo Method and Application to Spin Glass Simulations*J. Phys. Soc. Jpn.**65**pp. 1604-1608 (1996) - T. Okabe and M. Kawata and Y. Okamoto and M. Mikami:
*Replica-exchange {M}onte {C}arlo method for the isobaric-isothe rmal ensemble*Chem. Phys. Lett.**335**pp. 435-439 (2001) - Marvin Seibert, Alexandra Patriksson, Berk Hess and David van der
Spoel:
*Reproducible polypeptide folding and structure prediction using molecular dynamics simulations*J. Mol. Biol.**354**pp. 173-183 (2005) - David van der Spoel and M. Marvin Seibert:
*Protein Folding Kinetics and Thermodynamics from Atomistic Simulations*Phys. Rev. Lett.**96**pp. 238102 (2006) - H. X. Lei and Y. Duan:
*Improved sampling methods for molecular simulation*Curr. Opin. Struct. Biol.**17**pp. 187-191 (2007)

In case of questions please mail to **t-remd** at **xray.bmc.uu.se**.