[gmx-users] g_cluster cutoff

[Itamar Kass]

  Shalom Andreas,

I suggest you would look into the RMSD distribution inside your clusters 
(file namermsd-dist.xvg). In this file you will see one or more peak. 
The cut off you use should be larger then this peak but smaller then the 
second peak.

I know this is a bit simplicity, but for more you can search the mailing 
list.

Cheers,
Itamar

On 20/09/10 9:12 AM, Shay Teaching wrote:
> I'm not sure this is necessarily the case. Have you tried other 
> methods (gromos for example)? What are you getting when using other 
> methods?
> Regards,
> -Shay
>
> On Fri, Sep 17, 2010 at 6:14 PM, Kukol, Andreas <a.kukol at herts.ac.uk 
> <mailto:a.kukol at herts.ac.uk>> wrote:
>
>     Hi,
>
>     I am using g_cluster to analyse a trajectory (protein backbone):
>
>     g_cluster -f traj.xtc -s topol.tpr -g cluster.log -skip 10 -cutoff
>     0.5 -fit -method linkage
>
>     As a result I get almost hundred clusters. The plot of the RMSD
>     against time for the same trajectory generated with g_rms shows a
>     maximum RMSD just below 0.5 nm. Therefore, with a -cutoff of 0.5
>     nm, I would expect to find that the whole trajectory clusters into
>     ONE cluster. Am I expecting something wrong or is there a problem
>     with g_cluster ?
>
>     (using Gromacs 4.07)
>
>     Many thanks
>     Andreas
>
>
>     --
>     gmx-users mailing list gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://lists.gromacs.org/mailman/listinfo/gmx-users
>     Please search the archive at
>     http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>     Please don't post (un)subscribe requests to the list. Use the
>     www interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>

-- 


"In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut

===========================================
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: Itamar.Kass at monash.edu
============================================

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100920/5810907c/attachment.html>