[gmx-developers] GMX library functions and documentation

[Roland Schulz]

On Fri, Sep 14, 2012 at 11:58 AM, Ondrej Marsalek <ondrej.marsalek at gmail.com
> wrote:

> On Fri, Sep 14, 2012 at 5:02 PM, Roland Schulz <roland at utk.edu> wrote:
> >
> > The Gromacs 5 analysis tool framework is already documented very well
> > (
> http://jenkins.gromacs.org/job/Doxygen_Nightly_master/javadoc/html-user/group__module__trajectoryanalysis.html
> )
> > and the parts I'm using work very well. I personally would write new
> > analysis tools for Gromacs 5. If you want to try it out, you can get it
> from
> > git.
>
> I would very much like to do that, but I would also like to make the
> tool available to other users (of stable GMX) relatively soon. Is the
> new framework only getting released in 5.0, or already in 4.6?

It will not be release as part of 4.6. 5.0 might be release Aug 2013. See
http://redmine.gromacs.org/issues/949 for the preliminary planning.


> Are
> there any tools already available (like a rewrite of g_rdf or
> something similar) that I could read?

g_angel and g_select is available. You can run them with "g_ana
select(/angle)".


> I have seen the template, but a
> full tool would be nice. Also, what about support for time-dependent
> quantities, like MSD or time correlation functions?
>
Any computation which has a 1-1 mapping between the trajectory and the
output data doesn't require anything special. This should be true also
for MSD.
The need for extra computation which needs to happen after the per frame
computation is build in the concept. But only some functions (e.g.
averages, distances,  and histograms see
http://jenkins.gromacs.org/job/Doxygen_Nightly_master/javadoc/html-user/group__module__analysisdata.html)
are
implemented so far. It should be very easy to add a AnalysisDataModule
which computes correlation  functions (and it is certainly planned).

Roland


>
> Thanks,
> Ondrej
> --
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-developers-request at gromacs.org.
>
>
>
>
>


-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20120914/c13d6798/attachment.html>