Re: [AMBER] How to do clustering analysis by ptraj?

From: Biao Ma <jackyma1981.gmail.com>
Date: Tue, 24 Sep 2013 17:30:51 +0900

Thank you Thomas,

because my cpptraj is make some error

Fatal Error: This program was not built to run on the processor in your
system.
The allowed processors are: Intel(R) processors with Swing New Instructions
support.

maybe I should reinstall the AmberTools.

So, I use ptraj with 2drms command
> > trajin mdcrd 1 32500 25
> > 2drms out 2drms.gnu :2-103.CA
and product a 2drms.gnu file, that has some data, but I don't understand
the means of the data.

== 2drms.gnu ==
%!PS
 % -- define procedures --
 /inch {72 mul} def
 /box
 { newpath moveto
   0.0046 inch 0.0000 inch rlineto
   0.0000 inch 0.0046 inch rlineto
  -0.0046 inch 0.0000 inch rlineto
 closepath } def
 /fillbox { setgray fill } def
   1.2500 inch 1.2500 inch box
   1.0000 fillbox
   1.2500 inch 1.2546 inch box
   0.4951 fillbox
   1.2500 inch 1.2592 inch box
......
============
Could you tell me how can I use it to plot a 2Drms-plot by gnuplot?

Jacky



On Sat, Sep 21, 2013 at 2:42 AM, Thomas Cheatham <tec3.utah.edu> wrote:

>
> > However, I still have some question about how to use option "epsilon" and
> > "clusters".
> > Normally,* what case should we use "epsilon" or "clusters"?*
>
> Epsilon specifies the cutoff, and if epsilon is too small, you get many
> many clusters which is tricky to analyze / understand.
>
> There really isn't a case to specify which is better, it is simply a
> preference; essentially, clustering results depend on choices made in
> clustering algorithm, cutoff/epsilon, etc. and you want to run multiple
> variants of the clustering until you find a partitioning that helps
> explain your data.
>
> > *when I publish my result, is it necessary to analysis all frames?*
>
> Using the sieve doesn't miss frames, it just uses a subset to do the
> initial clustering and then puts the skipped points into existing
> clusters. As long as you do not miss a particular cluster with the sieve,
> results should be comparable to clustering over all frames. The way to
> check is to cluster multiple times (with different offsets, sieve sizes,
> and/or random frame sieving) to see how the results compare.
>
> > I created the 2D-rms plot as your advice.
> >
> > > trajin mdcrd 1 32500 25
> > > rms2d out 2drms.gnu :2-103.CA
> >
> > [image: Inline image 1]
> > This 2D-rms plot how can help us?
>
> Your plot is simply a 1D RMS and was likely calculated by ptraj NOT
> cpptraj. For ptraj you want the 2drms command.
>
> > In my case, "* **A snapshot may*
> > *become a member of its closest cluster if the rmsd is smaller*
> > *than a given cutoff (3 )." *described at the paper,
> > *if I want to do the same analysis with the paper to give a cutoff
> value,*
> > *should I set the epsilon option at the following input file ?*
>
> When you did this initially, you obtained more than 5000 clusters. If
> that is what you want, great...
>
> > Really, I did the clustering analysis used above input file, and compared
> > best 3 most
> > populated cluster's representative structure with the figure on the
> paper,
> > there are very different.
>
> Either your simulations are not converged or they were not converged in
> the published paper. I would compare the results from the different
> replicas (not temperature sorted) which if sufficient sampling was
> obtained should be identical.
>
> > *Maybe my initial extend structure at REMD simulation is not same with
> > paper's structure. If the others parameter is same, is it possible to get
> > the same result with published paper?*
>
> Yes, if both of you have demonstrated complete sampling (which is
> exceedingly difficult, especially for a disordered or semi-ordered
> protein)
>
> --tec3
>
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Received on Tue Sep 24 2013 - 02:00:04 PDT
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