[gmx-users] rmsd-dist.xvg

[Itamar Kass]

Thanks Xavier,

If I get a two picks graph, is this mean I have two distinct clusters? (for an
arbitrary RMS)?

Itamar.

Quoting "X.Periole" <X.Periole at rug.nl>:

> On Mon, 13 Feb 2006 08:53:56 +0200
>   Itamar Kass <ikass at cc.huji.ac.il> wrote:
> >
> > Shalom all,
> >
> > I am using g_cluster to analyze my MD results, where one
> >of the  output files is rmsd-dist.xvg.
> >
> > I hope this is not a silly question, but I do wish to
> >understand what  this graph represents.  Is this the RMS
> >distribution in the biggest  cluster? Is this the RMS
> >distribution among all clusters?
> >
>
> This is the distribution over the all matrix of rmsd in
> the
> ensemble you give (the trajectory).
>
> > Also, what a.u. represents?
> >
>
> atomic units ?? But it depends where you see it of course.
>
> >Finally, what can I learn from this graph on my results?
> >
>
> It tells you how the rmsds are distributed. You can use it
> to define your rmsd-based cutoff for clustering. I general
> I
> run the program twice. First to get the distribution and
> then with the appropriate cutoff.
>
> XAvier
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===========================================
| Itamar Kass
| The Alexander Silberman
| Institute of Life Sciences
| Department of Biological Chemistry
| The Hebrew University, Givat-Ram
| Jerusalem, 91904, Israel
| Tel: +972-(0)2-6585194
| Fax: +972-(0)2-6584329
| Email: ikass at cc.huji.ac.il
| Net: http://www.ls.huji.ac.il/~membranelab/itamar/itamar_homepage.html
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