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).
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. > -- *--------------------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.
