[gmx-developers] Bug in g_cluster/gmx_cluster

Roman Affentranger roman.affentranger at bc.biol.ethz.ch
Thu Jun 24 09:10:55 CEST 2004

Hi Berk

Thank you for your reply.

At 15:39 23.06.2004 +0200, you wrote:

>Looking at the code I guess you are right. But I could not reproduce the 

The program runs ok, but the cluster centers that are written to 
cluster.log/clusters.pdb are not the correct cluster centers.

>I had lots of trouble running g_cluster, as it often wrote an empty xpm file.
>I have worked on g_cluster several years ago, but after that there have
>been a lot of changes.
>Hopefully somebody else can fix this problem plus the writing of empty xpm 
>>Apart from that, I think that the clustering method denoted "linkage" does
>>not represent a full linkage, but rather a single linkage clustering.
>I programmed this and I think it does what is advertized in the g_cluster 
>-h help.
>So do you think (and if yes why) g_cluster does not do what is written in 
>the help?
>Or is full linkage not what has been written in the help?

As far as I recall, in full linkage clustering a structure would be added 
to a cluster if its distance to *all* other cluster members is below the 
cutoff. What is advertised in the g_cluster -h help is correct where it 
says "add a structure to a cluster when its distance to *any* element of 
the cluster is less than cutoff" (to me as a non-native english speaker 
this  means that the distance to only one cluster member needs to be below 
the cutoff  for a structure to be added to a cluster. Correct me if I'm 
wrong. At least that's what is done by the function 'gather', and this I 
think is called single linkage clustering).



Roman Affentranger
Swiss Federal Institute of Technology Zurich
Institute of Biochemistry
Schafmattstrasse 18
ETH Hoenggerberg HPM G 9.3
8093 Zurich
Phone: +41 1 632 31 39

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