[gmx-users] params for g_cluster and g_clustsize

[Erik Marklund]

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.
>
>
> 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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>
>
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-- 
-----------------------------------------------
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys