[gmx-users] fraction of native contacts calculation

[bipin singh]

Thanks a lot Oliver for the useful information.

On Fri, Nov 2, 2012 at 12:26 AM, Oliver Beckstein <obeckste at asu.edu> wrote:

> >>> Is there any way to calculate fraction of native contacts during the
> >>> simulation in gromacs. I searched the archives but didn't found any
> >>> significant clue.
> >>
> >> At present, there is no way to do this.  Likely one could modify the
> g_mindist code to do this - it would be a very nice feature.
> >>
> >
> > If one could get the -sel option of g_hbond to work again then you would
> get such information with -contact.
> >
>
> In the meantime you might be able to use MDAnalysis
> http://mdanalysis.googlecode.com/ and the native contact analysis in
> MDAnalysis.analysis.contacts, see
> http://packages.python.org/MDAnalysis/documentation_pages/analysis/contacts.html
>
> (If you have questions about MDAnalysis then please ask them on that
> project's discussion group
> http://groups.google.com/group/mdnalysis-discussion — people there are
> more than happy to help.)
>
> Best wishes,
> Oliver
>
> --
> Oliver Beckstein * oliver.beckstein at asu.edu
> http://becksteinlab.physics.asu.edu/
>
> Arizona State University
> Department of Physics
> Tempe, AZ 85287-1504
> USA
>
> Office: PSF 348
> Phone: +1 (480) 727-9765
> FAX: +1 (480) 965-4669
>
> Department of Physics:
> http://physics.asu.edu/home/people/faculty/oliver-beckstein
> Center for Biological Physics:
> http://biophysics.asu.edu/CBP/person.php?ID=343
>
>
>
>
>
>
> --
> 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
>



-- 
-----------------------
*Regards,*
Bipin Singh