Thanks a lot, your answer has been very useful!<div><br></div><div>Btw, do you know why is the default matrix used more often than the other? (I see that It's faster, but maybe there's another reason) <br><br><div class="gmail_quote">
On Mon, Jan 23, 2012 at 3:39 PM, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Victor,<br>
<br>
By default it does this:<br>
<div class="im"><br>
> for each frame f in traj1:<br>
> superimpose f with first frame<br>
><br>
> for each frame f1 in traj1:<br>
> for each frame f2 in traj2:<br>
> calculateRMSD f1, f2<br>
<br>
</div>But there's a hidden option -fitall that gives you the other. Check<br>
<br>
g_rms -h -hidden<br>
<div class="im"><br>
> I've also been trying to convert the resulting xpm file to a readable file<br>
> in order to process it using python. Is there any tool to do this kind of<br>
> conversion?(Btw I've been trying to find this kind of tool with not much<br>
> luck). There's enough info on the file to be able to parse it easily, but<br>
> using a 3rd party tested tool would be more convenient.<br>
<br>
</div>I posted a python script some while ago to do:<br>
<br>
<a href="http://lists.gromacs.org/pipermail/gmx-users/2010-October/054557.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/2010-October/054557.html</a><br>
<br>
Hope it helps,<br>
<br>
Tsjerk<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>
* Zernike Institute for Advanced Materials<br>
University of Groningen<br>
The Netherlands<br>
<font color="#888888">--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</font></blockquote></div><br><br clear="all"><div><br></div>-- <br><br>Víctor Gil Sepúlveda<br>E. Informatica - FIB - UPC<br>
</div>