[gmx-users] g_cluster output

sarbani chattopadhyay sarbani_c84 at rediffmail.com
Wed Apr 22 11:48:14 CEST 2009

    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.

Any suggestions regarding this will be very helpful.

Thanks in advance,
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