[gmx-users] Measurement of helical tilt (dimer tilt) using gmx helixorient

Roshan Shrestha roshanpra at gmail.com
Mon Jan 8 19:00:59 CET 2018

I want to measure the tilt of helix with the normal of bilayer. My system
is basically a dimer with two helices. Since using sidechain atom relative
to the axis is optional, I simply defined the index file of C-alpha atoms
of these two helices and measured the time evolution of tilt angle.
               Since it is a dimer system, I don't know how gmx helixorient
defines the helical axis and the axis of bilayer. Also, am I using the
command correctly or not to measure the angle of tilt of dimer ? The basic
command I've used for this is:
*gmx helixorient -s NPT_mut_0_eq.tpr -f mutant_nopbc.trr -n helix.ndx -b
100000 -e 150000 -oaxis -ocenter -orise -oradius -otwist -obending -otilt

Roshan Shrestha
M.Sc (Physics)
Central Department of Physics, Tribhuvan University
Kathmandu, Nepal

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