[gmx-users] Difference between equilibration and production run

[Neena Susan Eappen]

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