[gmx-users] Difference between equilibration and production run

Neena Susan Eappen neena.susaneappen at mail.utoronto.ca
Tue Jun 25 04:50:37 CEST 2019

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,

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