[gmx-users] params for g_cluster and g_clustsize

Dmitri Dubov ddubov at ngs.ru
Mon Jul 6 06:26:52 CEST 2009

In addition to previous letter (Monday is hard-day!)

It looks like I have known the answers to my questions.

Maybe the reason is that the g_cluster code compared to g_clustsize includes not only single linkage but also other algorithms. So the RMSD feature and smaller default value of -cutoff (which is unusual for single linkage) relate to other algorithms for cluster partitioning. Is it right?


> 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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С уважением,
 Dmitri                          mailto:ddubov at ngs.ru
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