[gmx-users] question regarding gmx helix orientation

[SHAHEE ISLAM]

hi,
i want to calculate the tilt angle of helix against the bilayer normal.
First i made a index file which contains the backbone of the residues of
large helix. I am using this command
*gmx helixorient -s *.tpr -f *.xtc -n helix.ndx -oaxis -ocenter -orise
-oradius -otwist -obending -otilt -orot*
my questions are

1. Should i mention any other residues in index file so that the angle can
be calculated along the bilayer normal.
2. by using this command i am able to analyse for 1 us coarse grained
simulation. But for the next 1 us run i am getting this error
"too many iterations in routine jacobi"
can anyone please guide me.
thanking you
shahee