[gmx-users] Calculating tilt angle with respect to the membrane normal

[zeineb SI CHAIB]

Dear GMX users,

I would like to calculate the angle of a transmembrane helix long axis with respect to the membrane normal and see how this angle fluctuates during the simulation.

In the forums, people were suggesting to use gmx helixorient. I used  it with the following command:

gmx helixorient -f trajectory.trr -s md.tpr -n index.ndx  -otilt tilt_TM1CA.xvg

and I choose the c-alpha of one transmembrane helix from the index file.

When I plotted the results of -otilt I obtained a weird graph with an angle equal to 0 during the entire simulation and this is not what I see when I visualize it.

I am not sure if I am using the tool in the correct way or if it is the right tool to use. If yes, how can gmx helixorient detect the membrane normal? and how can I interpret the results?

I would really appreciate if someone can help me with this.