During the equilibration step the heavy atoms are restrained..So.. You'll
not find any movement of these atoms... That's why you can not see that
On Tue 25 Jun, 2019, 8:21 AM Neena Susan Eappen, <
neena.susaneap...@mail.utoronto.ca> wrote:
> Hello gromacs users,
>
> I used NVT ensemble at constant temperature during
> both equilibration and data collection step. I observed that my peptide
> turned from extended coil to helical form only in the data collection step
> (very early on in the trajectory). Yes, a helical structure is
> theoretically expected for my peptide.
>
> However, I do not understand why I did not see this during equilibration.
> The observation is similar regardless of equilibration time.
>
> Any insight would be appreciated,
> Thank you,
> Neena
> --
> 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? 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.
