[gmx-users] Re: Re:g_cluster output

sarbani chattopadhyay sarbani_c84 at rediffmail.com
Thu Apr 23 10:36:34 CEST 2009

Actually I am not confused regarding the clustering method that is being used in default. I 
know that the method that is used is "Single linkage " method.

I got to know the options that I had used in my "g_cluster" command after going through 
g_cluster -h.

Regarding the command "g_cluster -cl -wcl" . it is written 
"-cl writes average (with option -av) or central structure of each cluster or
writes numbered files with cluster members for a selected set of clusters (with option -wcl, 
depends on -nst and -rmsmin). "

My question is how the average structure is obtained. I had written that it does not match 
with the members of the cluster, thus it signifies that it isn't writing that cluster member 
which is the cluster centre( determined through some criteria). 
It is not necessary for the average structure to be physically present in the cluster, but it is 
necessary to know how is it obtained. Moreover while going through the mailing lists, it was 
found that the average structures written by g_cluster were doubtful, though the Bug was 
reported to be removed.

I just wanted to know whether the representative structures of the clusters are correct or 

Thanks in advance,

On Wed, 22 Apr 2009 15:32:07 +0530 wrote
>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.
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