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
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