Provided by: gromacs-data_2025.2-1_all bug

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)
              Time of first frame to read from trajectory (default unit ps)

       -e <time> (0)
              Time of last frame to read from trajectory (default unit ps)

       -dt <time> (0)
              Only use frame when t MOD dt = first time (default unit ps)

       -xvg <enum> (xmgrace)
              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
       2025, GROMACS development team

2025.2                                            May 12, 2025                                GMX-HELIXORIENT(1)