Hi Junfang,<br>
<br>
It is not a problem that your molecule seems to be hanging out of the
box. Remember that the actual simulation system is infinitely stacked
and that that greater part of your molecule is simultaneously hanging
from a neighbouring box in your central one :)<br>
<br>
The jumps in RMSD can only be explained (at first glance) if you have a
multimer. In that case, if one part jumps, the RMSD will jump too.
Running trjconv with the option "-pbc nojump" can solve this.<br><br>
Cheers,<br>
<br>
Tsjerk<br>
<br><div><span class="gmail_quote">On 2/23/06, <b class="gmail_sendername"><a href="mailto:Junfang.Zhang@csiro.au">Junfang.Zhang@csiro.au</a></b> <<a href="mailto:Junfang.Zhang@csiro.au">Junfang.Zhang@csiro.au</a>> wrote:
</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Dear Gromacs users,<br><br><br>GROMACS prefers to keep a whole molecule connected and uses the first
<br>atom/protein group in the molecule as a reference position.<br><br>I used PBC in the simulation, but I found the large part of one polymer<br>chain is out of the simulation box. Is that a problem?<br><br><br>When I analyzed the RMSD, the points lay on three different curves, the
<br>lowest one goes to zero for zero time. The other two curves lie some<br>constant distance above it. It is most likely related to periodic<br>boundary conditions.<br><br>Can you please let me know how to solve these problems?
<br><br>Thank you in advance,<br><br>Junfang<br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">
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Groningen Biomolecular Sciences and Biotechnology Institute (GBB)<br>Dept. of Biophysical Chemistry<br>University of Groningen<br>Nijenborgh 4<br>9747AG Groningen, The Netherlands<br>+31 50 363 4336<br>