[gmx-users] analysis following the equlibration of protein-membrane system

[Olga Press]

Dear Gromacs users,
I've performed a membrane-protein simulation by charmm36ff as
described below:
1. 10ns of  NVT equilibration with position restrained on the protein
2. 50ns of NPT equilibration with position restrained on the protein
3. 200ns of  NPT equilibration without position restrained on the protein
Now I would like to calculate analyzes to ensure the stability and the
convergence of the simulation. So, my questions are:

1. Which analysis should I calculate? except for RMSD, the area per lipid,
bilayer-thickness, and temperature, pressure, total-energy, dimensions size
convergence?

2. I divided the equilibration into three parts as described above, should
I concatenate the .edr files from the *whole simulation* to make the
fixed.edr file (meaning from the beginning till the end (from NVT to
NPT_without restrains) in order to create the xvg files?

3. Following the equilibration of the whole system, I would like to run the
simulation itself. I'm working on a dimer (amyloid)-membrane system and I'm
interested in the interactions between the two attached monomers and the
membrane. Now my question is should I release the H-bond constraints in the
production step? and if so, what should I put at the constraints category
at the mdp file?  in this step I will not use the position restrains but
what about the H-bond constraints?

Thanks in advance
Olga