Hi George,<br><br>Recently I wrote an alternative, non-iterative clustering routine, that does not suffer from convergence failures. If you want, I can send you the modified trjconv source code. Note that it does not bother about the center of mass of the cluster, but just builds a network of neighbours, until there are no more. If you're clusters are not periodic, it won't matter.<br>
<br>Let me know...<br><br>Cheers,<br><br>Tsjerk<br><br><div class="gmail_quote">On Thu, Apr 14, 2011 at 4:48 PM, Erik Marklund <span dir="ltr"><<a href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a>></span> wrote:<br>
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jim jack skrev 2011-04-14 16.42:
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<td style="font: inherit;" valign="top">Dear GROMACS users,
<br>
<br>
I am trying to simulate an SDS micelle in water. As
simulation time goes by, the micelle approaches the edge
of the box and consequently some of these molecules get in
from the other side. This leads to incorrect radius of
gyration, eccentricity, etc. A solution to this problem is
the option <span style="font-style: italic;">trjconv -pbc
cluste</span>r as described in the page <a>http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering</a>.
In this case, the problem is that it takes a lot of time
and a huge file (several GB) is created due to this
procedure. Is there any other alternative?<br>
<br>
Thanks in advance<br>
<br>
George Koros<br>
<br>
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I don't think that the cluster option always converges. You could,
if your micelle is intact at frame 0, first do trjconv -pbc nojump,
then optionally trjconv -center. That should give a trajectory from
which you could calculate the radius of gyration. If SDS molecules
occationally leave the micelle and recombine with a priodic, then
you might have a problem with the suggested approach.<br>
<br>
<pre cols="72">--
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Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: <a href="tel:%2B46%2018%20471%204537" value="+46184714537" target="_blank">+46 18 471 4537</a> fax: <a href="tel:%2B46%2018%20511%20755" value="+4618511755" target="_blank">+46 18 511 755</a>
<a href="mailto:erikm@xray.bmc.uu.se" target="_blank">erikm@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se/" target="_blank">http://folding.bmc.uu.se/</a>
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<br>post-doctoral researcher<br>Molecular Dynamics Group<br>* Groningen Institute for Biomolecular Research and Biotechnology<br>* Zernike Institute for Advanced Materials<br>University of Groningen<br>The Netherlands<br>