ERROR: Some of your inputs are not numbers
ERROR: The lower limit of the temperature range has to be below the upper limit - Check your input!
ERROR: You must have temperatures that are > 0!
ERROR: You can not have zero atoms in protein!
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.