Hi,
The clusterout and clusterfmt keywords specify output cluster
trajectory filename prefix (<filename>.cX) and cluster file format
respectively. So you could do something like:
trajin md50.mdcrd.gzcluster C1 :1-1000 clusters 3 epsilon 4.0 out
cnumvtime.dat summary avg.summary.dat clusterout clustertraj
clusterfmt netcdf
Then in a second pass read in each clustertraj.cX trajectory and
calculate the average structure with the 'average' command. See the
manual for more details.
Also note that the clustering in ptraj currently has much more
functionality than cpptraj (more clustering algorithms, sieving etc)
so you may want to look at that as well.
-Dan
On Mon, Aug 20, 2012 at 1:01 AM, Catein Catherine
<askamber23.hotmail.com> wrote:
>
> Dear Amber Experts,
> I am trying to use the following commands in cpptraj to do clustering analysis for my trajectories.
> trajin md50.mdcrd.gzcluster C1 :1-1000 clusters 3 epsilon 4.0 out cnumvtime.dat summary avg.summary.dat
> I found three clusters afterwards in the dat files. I am trying to get a better understand about the average structure for each cluster. Can I do it with cpptraj? If yes, could you mind to teach me how to modify the above trajectories to get the file?
> Best regards,
> Catherine.
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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
(801) 585-9119 (Fax)
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Received on Mon Aug 20 2012 - 07:00:05 PDT
