[gmx-users] non-native contatcs

[bipin singh]

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.nagpal at 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-request at gromacs.org.
>



-- 



*--------------------Thanks and Regards,Bipin Singh*