Thank you for all your replies. Actually, I have already applied trjconv -pbc. So I'm sure that my analysis is on a whole protein, centered in my box. I'm using gromacs 4.0.3<br>So I think that you were right by saying that my dimer is not stable while my monomers are. But now, I have to fgure out why.<br>
<br>Thanks again,<br>Carla<br><br><div class="gmail_quote">On Wed, Jun 30, 2010 at 1:54 PM, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi,<br>
<div class="im"><br>
> Not necessary!<br>
> If the dimer separates across the boundaries you have<br>
> a problem of fitting the two together while they are separated.<br>
> This is only if you use the dimer. The monomers would be fine.<br>
<br>
</div>That was the case before gromacs 4. But the current versions don't<br>
keep molecules whole. This means that a PBC effect will show up in at<br>
least one monomer, if there is splitting over the boundaries. It also<br>
means that the jumps due to this are much smaller, and may not be as<br>
easily identified as before. That's a general word of caution,<br>
unrelated to the issue mentioned here.<br>
Concluding, if the version is <4, the increase in RMSD may either be<br>
due to splitting or due to relative motion of the domains, but the<br>
evolution of the RMSD (sudden or gradual) will tell which is the case.<br>
Otherwise, the increase will be due to relative motion of the domains.<br>
<br>
Cheers,<br>
<br>
Tsjerk<br>
<font color="#888888"><br>
<br>
--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
<br>
post-doctoral researcher<br>
Molecular Dynamics Group<br>
Groningen Institute for Biomolecular Research and Biotechnology<br>
University of Groningen<br>
The Netherlands<br>
</font><div><div></div><div class="h5">--<br>
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