VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Aug 16 2013 - 08:33:48 CDT

On Fri, Aug 16, 2013 at 8:39 AM, sunyeping <sunyeping_at_aliyun.com> wrote:
>
> Dear all,
> Is there anyone who is familiar the usage of measure cluster command and
> clustering plugin of vmd? According to the manual, the usage of measure
> cluster command should be:
>
> cluster selection [num numclusters] [distfunc flag] [cutoff cutoff] [first
> first] [last last] [step step] [selupdate bool] [weight weight]
>
> So I enter:
>
> measure cluster $sel num 5 disfunc fitrmsd first 1 last 2000
>
> But the results show that all the 2000 frames are grouped into one cluster:
> {1,2,3,... ....,2000} { } { } { } { } { }
>
> I have tried the change the option cutoff distfunc, but whatever I tried,
> the results are the same.

there is one important piece of information missing here. have you
looked at the RMSD of your configurations? how much is is fluctuating?
you cannot just pick some random numbers as input for the cluster
analysis, but have to make an informed choice.

>
> Have you meet the same circumstance? How to solve this problem?

you have to know what you are doing, then it will work.

> And if measure cluster is successul, how to apply the results to
> clustering plugin of VMD? Should they be the input of the third part
> software such as xcluster, R, etc.? The manual of this clustering plugin at
> http://physiology.med.cornell.edu/faculty/hweinstein/vmdplugins/clustering/
> seems doesn't ellustrate this clearly. Could some one explain this? Thanks
> in advance.

you have not read it correctly. the clustering plugin with *call*
measure cluster for you. nothing to integrate.

axel.

>
> Best regards,
>
> Yeping Sun
>
> Institute of Microbiology, Chinese Academy of Sciences 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.