[gmx-users] Difference between equilibration and production run

Bratin Kumar Das 177cy500.bratin at nitk.edu.in
Tue Jun 25 05:01:59 CEST 2019

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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