[gmx-users] representative structure using g-cluster

[David van der Spoel]

bmmothan at ucalgary.ca wrote:
> hello all,
> 
> I am trying to get the best representative structure of a 40ns MD of a 
> receptor to use for free energy calculations.
> 
> I want to have an idea what is the best way to do that.
> 
> I am using g_cluster with the gromos method. Is there a way to estimate
> the noise errors of the cluster analysis.
g_cluster will give you a representative structure for each cluster.

what do you mean with noise?
> 
> Thank you
> 
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-- 
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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