NAME

       g_helixorient - calculates local pitch/bending/rotation/orientation inside helices

       VERSION 4.6.5

SYNOPSIS

       g_helixorient  -s  topol.tpr  -f  traj.xtc  -n  index.ndx -oaxis helixaxis.dat -ocenter center.dat -orise
       rise.xvg -oradius radius.xvg -otwist twist.xvg -obending bending.xvg -otilt tilt.xvg  -orot  rotation.xvg
       -[no]h -[no]version -nice int -b time -e time -dt time -xvg enum -[no]sidechain -[no]incremental

DESCRIPTION

         g_helixorient  calculates  the coordinates and direction of the average axis inside an alpha helix, and
       the direction/vectors of both the Calpha and (optionally) a sidechain atom relative to the axis.

       As input, you need to specify an index group  with  Calpha  atoms  corresponding  to  an  alpha-helix  of
       continuous  residues.  Sidechain directions require a second index group of the same size, containing the
       heavy atom in each residue that should represent the sidechain.

        Note that this program does not do any fitting of structures.

       We need four Calpha coordinates to define the local direction of the helix axis.

       The tilt/rotation is calculated from Euler rotations, where  we  define  the  helix  axis  as  the  local
       x-axis,  the  residues/Calpha  vector  as   y, and the  z-axis from their cross product. We use the Euler
       Y-Z-X rotation, meaning we first tilt the helix axis (1)  around  and  (2)  orthogonal  to  the  residues
       vector,  and finally apply the (3) rotation around it. For debugging or other purposes, we also write out
       the actual Euler rotation angles as  theta[1-3].xvg

FILES

       -s topol.tpr Input
        Run input file: tpr tpb tpa

       -f traj.xtc Input
        Trajectory: xtc trr trj gro g96 pdb cpt

       -n index.ndx Input, Opt.
        Index file

       -oaxis helixaxis.dat Output
        Generic data file

       -ocenter center.dat Output
        Generic data file

       -orise rise.xvg Output
        xvgr/xmgr file

       -oradius radius.xvg Output
        xvgr/xmgr file

       -otwist twist.xvg Output
        xvgr/xmgr file

       -obending bending.xvg Output
        xvgr/xmgr file

       -otilt tilt.xvg Output
        xvgr/xmgr file

       -orot rotation.xvg Output
        xvgr/xmgr file

OTHER OPTIONS

       -[no]hno
        Print help info and quit

       -[no]versionno
        Print version info and quit

       -nice int 19
        Set the nicelevel

       -b time 0
        First frame (ps) to read from trajectory

       -e time 0
        Last frame (ps) to read from trajectory

       -dt time 0
        Only use frame when t MOD dt = first time (ps)

       -xvg enum xmgrace
        xvg plot formatting:  xmgrace,  xmgr or  none

       -[no]sidechainno
        Calculate sidechain directions relative to helix axis too.

       -[no]incrementalno
        Calculate incremental rather than total rotation/tilt.

SEE ALSO

       gromacs(7)

       More information about GROMACS is available at <http://www.gromacs.org/>.

                                                 Mon 2 Dec 2013                                 g_helixorient(1)