<br><br><div class="gmail_quote">On Fri, Sep 14, 2012 at 11:58 AM, Ondrej Marsalek <span dir="ltr"><<a href="mailto:ondrej.marsalek@gmail.com" target="_blank">ondrej.marsalek@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im">On Fri, Sep 14, 2012 at 5:02 PM, Roland Schulz <<a href="mailto:roland@utk.edu">roland@utk.edu</a>> wrote:<br>
><br>
> The Gromacs 5 analysis tool framework is already documented very well<br>
> (<a href="http://jenkins.gromacs.org/job/Doxygen_Nightly_master/javadoc/html-user/group__module__trajectoryanalysis.html" target="_blank">http://jenkins.gromacs.org/job/Doxygen_Nightly_master/javadoc/html-user/group__module__trajectoryanalysis.html</a>)<br>
> and the parts I'm using work very well. I personally would write new<br>
> analysis tools for Gromacs 5. If you want to try it out, you can get it from<br>
> git.<br>
<br>
</div>I would very much like to do that, but I would also like to make the<br>
tool available to other users (of stable GMX) relatively soon. Is the<br>
new framework only getting released in 5.0, or already in 4.6?</blockquote><div>It will not be release as part of 4.6. 5.0 might be release Aug 2013. See <a href="http://redmine.gromacs.org/issues/949">http://redmine.gromacs.org/issues/949</a> for the preliminary planning.</div>
<div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> Are<br>
there any tools already available (like a rewrite of g_rdf or<br>
something similar) that I could read?</blockquote><div>g_angel and g_select is available. You can run them with "g_ana select(/angle)". </div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I have seen the template, but a<br>
full tool would be nice. Also, what about support for time-dependent<br>
quantities, like MSD or time correlation functions?<br></blockquote><div>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.</div>
<div>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 <a href="http://jenkins.gromacs.org/job/Doxygen_Nightly_master/javadoc/html-user/group__module__analysisdata.html">http://jenkins.gromacs.org/job/Doxygen_Nightly_master/javadoc/html-user/group__module__analysisdata.html</a>) are implemented so far. It should be very easy to add a AnalysisDataModule which computes correlation functions (and it is certainly planned). </div>
<div><br></div><div>Roland</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Thanks,<br>
Ondrej<br>
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</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br>ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov">cmb.ornl.gov</a><br>865-241-1537, ORNL PO BOX 2008 MS6309<br>