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<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Thank you very much, Tsjerk.</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Regards,</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Junfang</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=MsoNormal style='margin-left:36.0pt'><font size=2 face=Tahoma><span
style='font-size:10.0pt;font-family:Tahoma'>-----Original Message-----<br>
<b><span style='font-weight:bold'>From:</span></b>
gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org] <b><span
style='font-weight:bold'>On Behalf Of </span></b>Tsjerk Wassenaar<br>
<b><span style='font-weight:bold'>Sent:</span></b> Thursday, 23 February 2006
5:39 PM<br>
<b><span style='font-weight:bold'>To:</span></b> Discussion list for GROMACS
users<br>
<b><span style='font-weight:bold'>Subject:</span></b> Re: [gmx-users] RMSD/Points
on different curves</span></font></p>
<p class=MsoNormal style='margin-left:36.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'> </span></font></p>
<p class=MsoNormal style='margin-right:0cm;margin-bottom:12.0pt;margin-left:
36.0pt'><font size=3 face="Times New Roman"><span style='font-size:12.0pt'>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</span></font></p>
<div>
<p class=MsoNormal style='margin-left:36.0pt'><span class=gmailquote><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'>On 2/23/06, <b><span
style='font-weight:bold'><a href="mailto:Junfang.Zhang@csiro.au">Junfang.Zhang@csiro.au</a></span></b>
<<a href="mailto:Junfang.Zhang@csiro.au">Junfang.Zhang@csiro.au</a>>
wrote: </span></font></span></p>
<p class=MsoNormal style='margin-left:36.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>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>
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<p class=MsoNormal style='margin-left:36.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'><br>
<br clear=all>
<br>
-- <br>
<br>
Tsjerk A. Wassenaar, M.Sc.<br>
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</span></font></p>
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