[gmx-users] Difference between equilibration and production run

[Bratin Kumar Das]

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.susaneappen at 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
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