[gmx-users] Re: gmx-users Digest, Vol 68, Issue 35
Mark Abraham
Mark.Abraham at anu.edu.au
Sun Dec 6 01:52:02 CET 2009
Stefan Hoorman wrote:
>
>
> 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?
I don't know, I've never seen them. I'd be expecting three numbers in
each to indicate a vector parallel to the axis.
> 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.
This is standard geometry - dot-products of vectors are related to the
cosine of the angle between them. Check wikipedia.
Mark
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