<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 href="mailto:a.kukol@herts.ac.uk">a.kukol@herts.ac.uk</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; 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>--<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
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