[gmx-users] Re: gmx-users Digest, Vol 68, Issue 35

[Stefan Hoorman]

>
> 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
>
> Ok, thank you for the info, but now I got a little bit confused. What
exactly does the info from axis1.dat, axis2.dat, axis3.dat and moi.dat mean?
And how would I use this info to calculate the helix tilt. I know the
general meaning of principal axes of inertia, but I could not find any
information more specific to this type of caltulation I need to do. If you
could give any reference or any other type of information a little bit more
specific I would be very greatful. I mean, if it is not too much to ask.
Thank you
Stef.
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