Thanks a lot Oliver for the useful information. On Fri, Nov 2, 2012 at 12:26 AM, Oliver Beckstein <obeck...@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.beckst...@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@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-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- ----------------------- *Regards,* Bipin Singh -- gmx-users mailing list gmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
