[gmx-users] g_cluster analysis

[Tsjerk Wassenaar]

Hi Sapna,

How should we know how many clusters you should have?

A cutoff of 0.2 is quite tight, and will give many clusters. Whether that's
what you want/need or whether that's meaningful/helpful for your goals is
something you should consider. We don't know what you're trying or doing.

Cheers,

Tsjerk

On Mon, May 23, 2016 at 9:03 AM, SAPNA BORAH <sapnauser365 at gmail.com> wrote:

> Dear all,
>
> I am trying to use g_cluster protocol to get representative snapshots of
> the simulations. I have concatenated 9 set of simulations and run g_cluster
> for the same. The result shows a total of 198 clusters.
>
> Is this correct?
>
> Following is the command I have used:
>
> g_cluster -s models.gro -f concatenated.xtc -dm rmsd-matrix.xpm -o
> clusters.xpm -sz cluster_size.xvg -clid cluster-id-over-time.xvg -cl
> all_clusters.pdb -cutoff 0.2 -method gromos
>
> Thanks in advance.
>
> Regards,
> Sapna.
>
> Sapna Mayuri Borah
> c/o Dr. A. N. Jha
> Research student
> Tezpur University,
> India
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-- 
Tsjerk A. Wassenaar, Ph.D.