[gmx-users] params for g_cluster and g_clustsize

[Dmitri Dubov]

Hi, Erik!

Many thanks for your exhaustive reply.

> Dmitri Dubov skrev:

>> 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.


> The rmsd is given in nm, and if the rmsd falls below the cutoff (also 
> given in nm, of course) the two frames are part of the same cluster when
> single lincage is used for g_cluster.

>> 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.

> Here's what I believe you've not quite grasped: g_cluster clusters 
> *frames* in a trajectory, generating groups of structures; g_clustsize
> clusters atoms/molecules *within each frame*. That said, the low default
> cutoff for g_cluster makes it less likely that you will end up with all
> frames in the same cluster, and the higher default cut-off for 
> g_clustsize is the typical hydrogen bond length and is useful for 
> finding water clusters, e.g. droplets in vacuo.

OK, I was using g_clustsize for similar aim. Not understanding g_cluster action I fell into idle trouble about correctness of my analysis.

>> 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?


> One would be clusters containing frames, the other clusters containing
> atoms/molecules. They are used for completely different things.

> /Erik

>> Thanks one more.

>> 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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-- 
Regards,
 Dmitri                          mailto:ddubov at ngs.ru
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