Maybe this will help or at least provide some initial insights. The down side is that it is somewhat generic. So please if someone has something in mind, please share the name of the research.

http://dasher.wustl.edu/bio5476/reading/methenzymol-383-119-04.pdf

Here are 2 links, which might be helpful :

http://www.gromacs.org/Documentation/How-tos/REMD

http://folding.bmc.uu.se/remd/

The 2 Basic papers on REMD :

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)

-- Emanuel

I would start with searching PubMed (Filters: Review, English) using the following query:

"replica exchange"[title/abstract] and "protein"[title/abstract]

---

http://www.ncbi.nlm.nih.gov/pubmed

---

13 hits . . .

Thank you all so much, I will check these and let you know

Hello Sotiris, The number of replicas would be related to the square root of the number of atoms and the temperature distribution (temperature range between 270 - 600K) would be chosen to be a geometric progression. You can follow the procedure based on http://ambermd.org/tutorials/advanced/tutorial7/index.htm

Best regards

Bahareh

hi all sorry for several messages,I was getting error message while I was struggling to send my response and suddenly observed them all.

Thanks Bahareh, very helpful, don't mind the messages