Hello all,
Read the .txt file that is generated by ptraj. There are a few lines in
there that look like this:
X....X....XXXX......
.XXXX.XXXX....XXXXXX
In this case this means that there are two clusters and that there are 20
snapshots. Each X is a snapshot that belongs to each cluster. For example:
Snapshot 1 belongs to cluster 0, snapshots 2-5 belong to cluster 1, and so
forth. I suggest you to write your own parsing code to associate the
snapshot/cluster correlation and group the original snapshots present in the
simulation.trj by cluster.
Hope it helps,
Joćo
On Wed, Feb 16, 2011 at 4:42 AM, Massimiliano Porrini <M.Porrini.ed.ac.uk>wrote:
> 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> 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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>
--
Joćo Henriques, MSc in Biochemistry
Faculty of Science of the University of Lisbon
Department of Chemistry and Biochemistry
C8 Building, Room 8.5.47
Campo Grande, 1749-016 Lisbon, Portugal
E-mail: joao.henriques.32353.gmail.com / jmhenriques.fc.ul.pt
http://intheochem.fc.ul.pt/members/joaoh.html
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Received on Wed Feb 16 2011 - 21:00:02 PST
