Hi,
This information is in [outfile].txt. The first part of this file will
contain some general information about the clustering algorithm used
and some stats on the clusters themselves. Then there will be a line
like:
#Clustering: <X> clusters
where X is the total number of clusters, followed by X lines
specifying which frames belong to that cluster. For example, say you
have 3 clusters and 5 frames; you may get something like:
#Clustering: 3 clusters
.XX..
...XX
X....
In this case frame 1 is in cluster 3, frames 2-3 are in cluster 1, and
frames 4-5 are in cluster 2.
If you use cpptraj, cluster number vs time is printed to the 'out
<file>' by default. However, cpptraj clustering does not currently
have all of the features of ptraj clustering.
Hope this helps,
-Dan
On Fri, Oct 26, 2012 at 6:08 AM, Chiara Pallara <chiara.pallara.bsc.es> 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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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
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Received on Fri Oct 26 2012 - 07:30:03 PDT
