Temperature generator for REMD-simulations

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.

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.

Exchange probability: Tolerance:
Lower temperature limit: Upper temperature limit:
Number of water molecules: Constraints in water:
Number of protein atoms: Constraints in the protein:
Hydrogens in protein: Virtual sites in protein:
Simulation type:

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].

  1. K. Hukushima and K. Nemoto: Exchange Monte Carlo Method and Application to Spin Glass Simulations J. Phys. Soc. Jpn. 65 pp. 1604-1608 (1996)
  2. 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)
  3. 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)
  4. David van der Spoel and M. Marvin Seibert: Protein Folding Kinetics and Thermodynamics from Atomistic Simulations Phys. Rev. Lett. 96 pp. 238102 (2006)
  5. 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.