Once you identify the number and identity of the non-native contacts (after comparing the two matrices), then you can extract the probability of their formation from your trajectory.
On Mon, Jan 20, 2014 at 8:23 PM, suhani nagpal <suhani.nag...@gmail.com>wrote: > okay. > > Basically i want to make a plot these non-native contacts information which > are formed. > > some insights please > > Thanks > > > On Mon, Jan 20, 2014 at 7:33 PM, bipin singh <bipinel...@gmail.com> wrote: > > > >so, now I need to compare the two contact matrices? ( one of native and > > >the other after 200ns) > > >as in superimpose or just by observing? > > In principle yes, you can get it both way i.e. by comparing the two > > matrices visually or mathematically, it depends what information you are > > looking for. > > > > > > On Mon, Jan 20, 2014 at 5:36 PM, suhani nagpal <suhani.nag...@gmail.com > > >wrote: > > > > > Hey Bipin > > > > > > Thanks. yes, I have calculated the native contacts as well as the > > fraction > > > of native contacts using the vmd extension earlier. > > > > > > so, now I need to compare the two contact matrices? ( one of native > and > > > the other after 200ns) > > > > > > as in superimpose or just by observing? > > > > > > Thanks > > > > > > > > > On Wed, Jan 15, 2014 at 10:16 PM, rajat desikan < > rajatdesi...@gmail.com > > > >wrote: > > > > > > > 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_Listbefore > > > > > >>> 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-usersor > > > > > >>> 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-usersor > > > > > > 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-usersor > > > > > 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-usersor > > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > -- > > > 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. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? 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