Hi I want to perform an remd simulation of a large protein system. The bibliography I found so far is about small systems and doesn't describe the way they decide on the number of replicas or the diferent temperature values. Is there a scientific paper on how to perform this or at least any good papers on REMD and large protein systems? Thanks in advance.
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]
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http://www.ncbi.nlm.nih.gov/pubmed
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13 hits . . .
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.
You are welcome Sotiris, you may also see http://folding.bmc.uu.se/remd/ and read:
Y. Sanbonmatsu and A. E. Garcia, “Structure of Met-Enkephalin in Explicit Aqueous Solution Using Replica Exchange Molecular Dynamics.” Proteins, 46, 225-234 (2002).
A. Patriksson & D. van der Spoel, “A temperature predictor for parallel tempering simulations.” Phys. Chem. Chem. Phys., 10, 2073-2077 (2008).
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