[gmx-users] rmsd-dist.xvg

[Daniela S. Mueller]

hi,

as the distribution of the rmsds is a projection of all rmsds on a 
(one-dimensional) distance, you can't tell if they belong from one or 
more clusters and therefore one or more minima.

i think xavier is right with his careful statement.

in this distribution, smaller peaks can be hidden under your sum of 
peaks, depending on your sample. better experiment a little with the 
cutoff.

BEWARE: there was a bug in g_cluster. see earlier mailing list 
contributions about that and fix it first, if you want to use it for 
clustering.

success!
daniela


Tsjerk Wassenaar wrote:
> 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 
> <mailto: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 <mailto: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>
>     ============================================
> 
> 
> -- 
> 
> 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
> 
> 
-- 

Daniela S. Mueller

Diplom biologist
______________________________________________________________________

-Molecular Dynamics Group, UQ -

Address:
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Phone: +61-7-33653732
Email: d.s.mueller at uq.edu.au

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**********************************************************************

- MD group, RuG -

Address:
Molecular Dynamics
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747 AG Groningen
The Netherlands

Email: d.s.mueller at rug.nl

Website: http://www.rug.nl/gbb/md
______________________________________________________________________