[gmx-users] g_cluster output

[Mark Abraham]

sarbani chattopadhyay wrote:
> Hi,
> 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" 
> structure.

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 
physical either.

Mark