NAME

       gmx-helixorient - Calculate local pitch/bending/rotation/orientation inside helices

SYNOPSIS

          gmx helixorient [-s [<.tpr>]] [-f [<.xtc/.trr/...>]] [-n [<.ndx>]]
                       [-oaxis [<.dat>]] [-ocenter [<.dat>]] [-orise [<.xvg>]]
                       [-oradius [<.xvg>]] [-otwist [<.xvg>]]
                       [-obending [<.xvg>]] [-otilt [<.xvg>]] [-orot [<.xvg>]]
                       [-b <time>] [-e <time>] [-dt <time>] [-xvg <enum>]
                       [-[no]sidechain] [-[no]incremental]

DESCRIPTION

       gmx  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

OPTIONS

       Options to specify input files:

       -s [<.tpr>] (topol.tpr)
              Portable xdr run input file

       -f [<.xtc/.trr/...>] (traj.xtc)
              Trajectory: xtc trr cpt gro g96 pdb tng

       -n [<.ndx>] (index.ndx) (Optional)
              Index file

       Options to specify output files:

       -oaxis [<.dat>] (helixaxis.dat)
              Generic data file

       -ocenter [<.dat>] (center.dat)
              Generic data file

       -orise [<.xvg>] (rise.xvg)
              xvgr/xmgr file

       -oradius [<.xvg>] (radius.xvg)
              xvgr/xmgr file

       -otwist [<.xvg>] (twist.xvg)
              xvgr/xmgr file

       -obending [<.xvg>] (bending.xvg)
              xvgr/xmgr file

       -otilt [<.xvg>] (tilt.xvg)
              xvgr/xmgr file

       -orot [<.xvg>] (rotation.xvg)
              xvgr/xmgr file

       Other options:

       -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>
              xvg plot formatting: xmgrace, xmgr, none

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

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

SEE ALSO

       gmx(1)

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

COPYRIGHT

       2015, GROMACS development team