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:[email protected]
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