[gmx-users] gmx gangle : How to calculate the angle between a vector and Z axis?

[Vikas Dubey]

Dear all,

I have been trying to use gmx gangle for the calculation of the following
angle :
I have a group of 3 residues and another group of 4 residues. I want to
define a vector which goes through the center of mass of these two groups
and I am interested in calculating the angle  of the vector w.r.t to the
Z-axis, which seems doable from the gmx gangle.
based on the documentation, I write the following :

*gmx angle -f traj.xtc -s topol.tpr -n index.ndx -g1 -vector -g2 z -group1
<contains-all-the-atoms-in-aboved-mentioned-groups> -seltype res_com
-selrpos -res_com -oav -all   *

but I don't think this is correct because I am calculating the center of
mass of whole group. Is there a way to calculate this angle?

Thanks,