[gmx-users] g_helixorient help

[rajat desikan]

Hi All,
I am trying to calculate the angle between the axes of two alpha helices
(say A and B) in my simulation. I have separate index files for the
residues pertaining to each helix.

I calculated the tilt.xvg for both A and B. The output is slightly
confusing. tilt_A.xvg when viewed with xmgrace -nxy shows 27 data sets.
What do these correspond to? (Helix A has 34 residues). Similarly for
bending_A.xvg

How do I go about this? Is this the right way to calculate the relative
helix axis angle?

Thanks,

-- 
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore