[gmx-users] remd and nmr

[David van der Spoel]

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.
________________________________________________________________________
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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