[gmx-users] g_bundle!

[Marc F. Lensink]

On Wed, Jun 20, 2007 at 07:27:42AM -0700, priyanka srivastava wrote:
> Dear All,
> 
> I want to calculate tilt angle of a peptide inserted
> inside the lipid bilayer (i.e. angle between the
> helical axis and bilayer normal). From previous posts
> I got an idea that g_bundle wud solve my problem.

hm, g_helixaxis will do the trick:

(from the help)
"Output is given through -o in the following format:

 time  i  dir(x) dir(y) dir(z)  length  rms  cos(z) groupname
   time      - time (ps)
   i         - axis index (0..nh-1)
   dir(xyz)  - axis vector component
   length    - axis length
   rms       - rms of atom coordinates from helix axis
   cos(z)    - the cosine of the angle with the z-axis
   groupname - name of index group defining the helix"

in time this will appear on
http://www.scmbb.ulb.ac.be/Users/lensink/lipid, for now you'll have to
contact me off-list for the distribution.

cheers,
marc