Re: [AMBER] Trajectory Clustering

From: Gustavo Seabra <>
Date: Fri, 26 Oct 2012 09:39:06 -0300

Hi Chiara,

I don't think there is such information. What you can do is, based on the relative number of structures in each cluster, estimate the percentage of the total time spent sampling that area of space. To see the members, you can just look at the output trajectories in a program like VMD.

Gustavo Seabra
Professor Adjunto
Departamento de Química Fundamental
Universidade Federal de Pernambuco
Recife - PE - Brasil
+55-81-2126-7450 x5023

On Oct 26, 2012, at 9:08 AM, Chiara Pallara wrote:

> Hi,
> I clustered the frames of my trajectory into 10 clusters with the
> command cluster of ptraj module.
> I applied the averagelinkage algorithm on the alpha carbons of my sistem
> using this command:
> cluster out [outfile] representative pdb average pdb averagelinkage
> clusters 10 rms .CA
> Now I would to know the MD times of the each cluster representative and
> its members. Do you know where I can find this information? I did not
> find nothig about in the output file.
> Thanks
> Chiara
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