[gmx-users] params for g_cluster and g_clustsize

Dmitri Dubov ddubov at ngs.ru
Mon Jul 6 05:53:07 CEST 2009

Thanks, David.

Sorry, maybe my questions were too fuzzy.

They concern the definition of cluster in these codes.
1) When we estimate through single linkage whether the structure belongs to the cluster we should find the smallest distance between any element of the structure and any element of cluster, then compare this distance with the cutoff value. I don't understand how this cutoff value may have "root mean square deviation" feature.

2) To my knowledge the g_clustsize uses the same "single linkage" algorithm for cluster construction. If so, there should be the similar cut-off parameter. The -cut option looks like this one. But very different default values of these parameters (cutoff=0.1 in g_cluster and cut=0.35 in g_clustsize) are doubted to me. 

These two questions may be reformulated to single one:
If I would apply these two codes (using single linkage with default values) to the same system how different would be the cluster partitions?

Thanks one more.

> Dmitri Dubov wrote:
>> Dear gmx'ers,

>> Could you explain me the following points in manuals for g_cluster and 
>> g_clustsize programs?

>> 1) Manual for g_cluster:

>> "single linkage: add a structure to a cluster when its distance to any 
>> element of the cluster is less than cutoff...

>> Other options...

>> -cutoff real 0.1 RMSD cut-off (nm) for two structures to be neighbor"

>> What does "RMSD" mean here?
> Root mean square deviation. Typical for proteins.

>> 2) Manual for g_clustsize:

>> "-cut real 0.35 Largest distance (nm) to be considered in a cluster"

>> Is there any difference between -cut and -cutoff in g_cluster above?

> These are two different programs, unfortunately not sharing any code.

>> Thanks.

>> Dmitri

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