[gmx-users] rmsd-dist.xvg

X.Periole X.Periole at rug.nl
Mon Feb 13 09:24:32 CET 2006

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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