[gmx-users] rmsd-dist.xvg

[Tsjerk Wassenaar]

Hi Itamar,

One peak indicates that it's likely you're only sampling a single local
minimum.

Tsjerk

On 2/13/06, Itamar Kass <ikass at cc.huji.ac.il> wrote:
>
>
> On Feb 13, 2006, at 11:09 AM, X.Periole wrote:
>
> To get the number of clusters you have to run the program
>
> again giving a cutoff, the minimum between the picks or
>
> another one.
>
>
> Here I probably have to ask, if I have only one pick, should I chose a
> rmsd cutoff from the right slope of the graph? Is one pick indicates
> unnatural uniform simulation?
>
> ===========================================
> | 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
> | Homepage:
> http://www.ls.huji.ac.il/~membranelab/itamar/itamar_homepage.html<http://www.ls.huji.ac.il/%7Emembranelab/itamar/itamar_homepage.html>
> ============================================
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--

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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