Temperature generator for T-REMD simulations

Note by Jicun Li 2021-09-29: This page contains an online tool to generate temperatures for T-REMD calculations. It is based on the php version of the same tool (code was downloaded from https://github.com/dspoel/remd). I tranlated it to a javascript version, because the original tool is not availble sometimes. This version does not depend on any webserver, and is expected to work any time, In fact, you can save the page to your computer and it will work locally. However, I did tested it on Chrome only, so please use it with Chrome first.

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 tool 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 T-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.


Setup for NPT simulations
Exchange probability Desired  
Tolerance
Temperature limit (K) Lower    
Upper    
Water Number of molecules
Constraints used   
Protein Number of atoms   
Hydrogens used    
Virtual sites used
Constraints used  


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.