Hi Tsjerk,<br><br>thank you for your answer.<br>Actually, for the initial structure, I took the values of the B factor, and calculated the mean square displacement per atom. This is what I meant by saying RMSF of initial structure. Anyway, thanks for the explanation.<br>
<br>But I have another question: I need to take 3 structures and make an average structure of these 3. Is there a way to do it with gromacs?<br><br>Cheers,<br>Carla <br><br><br><div class="gmail_quote">On Thu, Jun 10, 2010 at 12:15 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 Carla,<br>
<div class="im"><br>
On Thu, Jun 10, 2010 at 12:03 PM, Carla Jamous <<a href="mailto:carlajamous@gmail.com">carlajamous@gmail.com</a>> wrote:<br>
> Hi Everyone,<br>
><br>
> please I have a question concerning g_rmsf.<br>
> I need to compare the RMSF from my initial structure to the RMSF of my<br>
> average structure.<br>
<br>
</div>Single structures (initial c.q. average) do not have an RMSF.<br>
<div class="im"><br>
> When I did<br>
><br>
> g_rmsf -s .tpr -f .xtc -n .ndx -b xx -e yy -o rmsf<br>
><br>
> or<br>
><br>
> g_rmsf -s .tpr -f .xtc -n .ndx -b xx -e yy -res -o rmsf<br>
<br>
</div>This is not what you did. Please copy/paste command lines.<br>
<div class="im"><br>
> I got the same result, when choosing C-alpha for root mean square<br>
> calculation.<br>
<br>
</div>Sure, when selecting C-alphas, averaging the RMSF per residue<br>
(sum_over_calphas_in_residue/number_of_calphas_in_residue) will<br>
evidently be identical to calculating the RMSF on an atom basis for<br>
each Calpha.<br>
<div class="im"><br>
> So please can anyone explain how can I get the average per residue over a<br>
> period of time?<br>
<br>
</div>Select 'protein' (and use the -res flag).<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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