Hi, I have never done this before. But is this a possibility? http://www.pymolwiki.org/index.php/Contact_map_visualizer
On Wed, Jan 15, 2014 at 8:41 PM, bipin singh <bipinel...@gmail.com> wrote: > Hello Dr. Justin, > > Yes, there is no in-built module in Gromacs to get the information about > native contacts during the simulation, but I think it can be done using the > following resources outside the Gromacs: > > > http://pythonhosted.org/MDAnalysis/documentation_pages/analysis/contacts.html > > http://www.multiscalelab.org/utilities/RMSDTTNC > > > On Wed, Jan 15, 2014 at 7:38 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > > > > On 1/15/14, 7:11 AM, bipin singh wrote: > > > >> First define and calculate the native contacts (contacts which were > >> present > >> in native reference structure and exist for significant amount of time > >> during simulation). Then you can identify the contacts which exist for > >> significant amount of time but were not present in native reference > >> structure (which may correspond to non-native contacts). > >> > >> > > Can you actually do this within Gromacs, or outside software? I'd be > > curious to know. > > > > -Justin > > > > > > > >> > >> On Wed, Jan 15, 2014 at 1:05 PM, suhani nagpal <suhani.nag...@gmail.com > > > >> wrote: > >> > >> Greetings > >>> > >>> I'm studying protein unfolding by CTMD and REMD simulations to capture > >>> the > >>> intermediate states. > >>> > >>> I want to calculate the non-native contacts formed during the > >>> intermediate > >>> state. > >>> > >>> Suggestions please > >>> > >>> > >>> Thanks > >>> Suhani > >>> Proteomics and Structural biology Lab > >>> CSIR-IGIB > >>> -- > >>> Gromacs Users mailing list > >>> > >>> * Please search the archive at > >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >>> posting! > >>> > >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>> > >>> * For (un)subscribe requests visit > >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >>> send a mail to gmx-users-requ...@gromacs.org. > >>> > >>> > >> > >> > >> > > -- > > ================================================== > > > > Justin A. Lemkul, Ph.D. > > Postdoctoral Fellow > > > > Department of Pharmaceutical Sciences > > School of Pharmacy > > Health Sciences Facility II, Room 601 > > University of Maryland, Baltimore > > 20 Penn St. > > Baltimore, MD 21201 > > > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > > > ================================================== > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at http://www.gromacs.org/ > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > -- > > > > *--------------------Thanks and Regards,Bipin Singh* > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.