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
> 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:[email protected]
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