>>> 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
