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Shalom Andreas,<br>
<br>
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.<br>
<br>
I know this is a bit simplicity, but for more you can search the
mailing list.<br>
<br>
Cheers,<br>
Itamar<br>
<br>
On 20/09/10 9:12 AM, Shay Teaching wrote:
<blockquote
cite="mid:AANLkTi=bPmPhBkHu3UWsfdwLTnKU8ANkfGYoV-0q4v8X@mail.gmail.com"
type="cite">
<div dir="ltr">
<div>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?</div>
<div>Regards,</div>
<div>-Shay<br>
<br>
</div>
<div class="gmail_quote">On Fri, Sep 17, 2010 at 6:14 PM, Kukol,
Andreas <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:a.kukol@herts.ac.uk">a.kukol@herts.ac.uk</a>></span>
wrote:<br>
<blockquote style="border-left: 1px solid rgb(204, 204, 204);
margin: 0px 0px 0px 0.8ex; padding-left: 1ex;"
class="gmail_quote">Hi,<br>
<br>
I am using g_cluster to analyse a trajectory (protein
backbone):<br>
<br>
g_cluster -f traj.xtc -s topol.tpr -g cluster.log -skip 10
-cutoff 0.5 -fit -method linkage<br>
<br>
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 ?<br>
<br>
(using Gromacs 4.07)<br>
<br>
Many thanks<br>
Andreas<br>
<font color="#888888"><br>
<br>
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</blockquote>
<br>
<pre class="moz-signature" cols="72">--
"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: <a class="moz-txt-link-abbreviated" href="mailto:Itamar.Kass@monash.edu">Itamar.Kass@monash.edu</a>
============================================</pre>
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