[gmx-users] remd and nmr

andrea spitaleri spitaleri.andrea at hsr.it
Fri Jan 26 12:22:11 CET 2007

Hi all,
I am trying to perform a REMD simulation on a small cyclic peptide (7 aa). I have calculated a 
plausible structure by cns using NOEs data leading to 4 clusters with a cutoff of 0.1 nmr and each 
of them satisfy the NOEs' restraints. However, since it is a small peptide the NOEs could rise from 
an average of interactions between the few aminoacid and therefore the final structure in one of the 
existing in solution.
Now, I am wondering whether the "quality" of the starting point given to a REMD simulation could in 
somehow bias the final results. Basically, I am thinking to feed into gromacs one of this structure 
(the  best in procheck_nmr) and to see whether the REMD simulation might explore also the other 
configurations found by cns and give much more clue on the relative stabilty.

Any suggestion?

thanks in advance

Andrea Spitaleri PhD
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)

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