[gmx-users] quality of cluster strucutres

David van der Spoel spoel at xray.bmc.uu.se
Wed Jun 14 23:05:25 CEST 2006

Mauricio Sica wrote:
> Dear all
> I´ve obtained one cluster structure from a protein simulation. Then, as I
> wanted to use this structure as a static model, I checked it with WHAT_IF
> and the result was that as a model is a little poor (a list of bad angles,
> bad distances, problems with planarity and so on as you can imagine). I
> decided to minimize it .So, I performed simulated annealing (300>360>300)
> PRMD (only C_alfas in posre.itp) and then minimization. But the model
> continues didn't improve. I know this would be expected for a "particular"
> conformation at a " particular" moment during the simulation.
> Have any one of you any suggestion?
you don't say HOW you got the structure

g_cluster -method gromos suggests a "real" structure from the trajectory 
as best representative for each cluster.

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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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