[gmx-users] g_cluster output
Mark.Abraham at anu.edu.au
Wed Apr 22 12:00:30 CEST 2009
sarbani chattopadhyay wrote:
> I have a query regarding "g_cluster" output.
> I gave the command
> g_cluster -f ../const_temp_20ns_0.pdb -s ../../md_0.tpr -sz -tr -cl -wcl
> 25 -cutoff 0.2
> It is written in the "clusters.log" file that the middle structures of
> each cluster is written in the
> "clusters.pdb" file.
> How is this "middle structure" obtained ? The coordinates of the middle
> structure do not match
> with any of the structures in that particular cluster. Is the " middle "
> structure same as the
> "average " structure. if so what is the criteria to get the "middle"
Start with g_cluster -h. That will tell you what the default clustering
algorithm you're using is, which may in turn indicate what the "middle"
of a cluster might mean. Obviously an average structure need not be a
member of the set (just as for a set of numbers) and need not be
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