[gmx-users] About g_rms and the XPM file format

[Víctor]

Thanks a lot, your answer has been very useful!

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)

On Mon, Jan 23, 2012 at 3:39 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Victor,
>
> By default it does this:
>
> > for each frame f in traj1:
> >   superimpose f with first frame
> >
> > for each frame f1 in traj1:
> >   for each frame f2 in traj2:
> >     calculateRMSD f1, f2
>
> But there's a hidden option -fitall that gives you the other. Check
>
> g_rms -h -hidden
>
> > I've also been trying to convert the resulting xpm file to a readable
> file
> > in order to process it using python. Is there any tool to do this kind of
> > conversion?(Btw I've been trying to find this kind of tool with not much
> > luck). There's enough info on the file to be able to parse it easily, but
> > using a 3rd party tested tool would be more convenient.
>
> I posted a python script some while ago to do:
>
> http://lists.gromacs.org/pipermail/gmx-users/2010-October/054557.html
>
> Hope it helps,
>
> Tsjerk
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 

Víctor Gil Sepúlveda
E. Informatica - FIB - UPC
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120123/20d8ee57/attachment.html>