[gmx-users] Re:Re: helix tilt

[Mark Abraham]

Stefan Hoorman wrote:
> 
>     Stefan Hoorman wrote:
>      > How can I calculate the angle between a helix inserted in a
>     membrane and
>      > the axis perpendicular to the surface of the membrane. I have tried
>      > using g_helixorient, but the graphs all come as a straight line
>     in zero.
> 
>     See -z in g_sgangle -h
> 
>     Mark
> 
> 
> Thank you for the tip, but again I faced a problem. I could only analyse 
> using g_sgangle with an index group containing 3 atoms. Then the problem 
> is, since my helix not only tilts, but also it bends a little back and 
> forth, the angle between it and the z axis will vary greatly depending 
> on which three atoms I choose. I imagined that by choosing three alpha 
> carbon atoms every four residues would give me a good outcome, but it 
> turns out that the angle changes a lot, and I am guessing it is because 
> of this bending movement. When I say "changes a lot" I mean; it starts 
> at 0º and gets up to 50º, which i imagine to be a little bit too much.
> Would there be a better way to calculate this?

g_principal will calculate the axes of inertia, from which you can 
calculate the angle with the Z-axis.

Mark