ikass at cc.huji.ac.il
Mon Feb 13 09:55:18 CET 2006
If I get a two picks graph, is this mean I have two distinct clusters? (for an
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
> 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
> run the program twice. First to get the distribution and
> then with the appropriate cutoff.
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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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