Hello,
What you call "clust_out.rep.c0" is the closest structure to the
cluster 0 centroid
(you named it cluster 1).
What I would do to catch the frame related to this structure is to calculate
and plot the RMSD with this structure as reference, e.g. for the backbone atoms:
trajin "mdcrd_file"
reference clust_out.rep.c0
rms reference mass out "rms_file.out" .C,CA,N
>From the graph you should get an RMSD = 0 only for one structure,
this is the frame you are looking for.
Probably there is a faster and simpler way to do that.
Cheers,
MP
2011/2/16 475649770 <475649770.qq.com>:
> Dear professors:
> I clustering my system using the ptraj module, and the program produced the file like "clust_out.rep.c0" as the represent structure of the cluster 1. I wanted to know that which snapshot this structure extracted from. I think this represent structure is the centroid of the cluster 1, I want to know which snapshot it is at the MD trajectory.
> Thank you!
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--
Dr Massimiliano Porrini
P. E. Barran Research Group
Institute for Condensed Matter and Complex Systems
School of Physics & Astronomy
The University of Edinburgh
James Clerk Maxwell Building
The King's Buildings
Mayfield Road
Edinburgh EH9 3JZ
Tel +44-(0)131-650-5229
E-mails : M.Porrini.ed.ac.uk
mozz76.gmail.com
maxp.iesl.forth.gr
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Received on Wed Feb 16 2011 - 05:00:02 PST
