[gmx-users] remd and nmr

David van der Spoel spoel at xray.bmc.uu.se
Fri Jan 26 13:11:26 CET 2007

andrea spitaleri wrote:
> 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
Since you are going to do many replicas you can use all structures and 
see whether one is favored. You could even use this with restraints on.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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