GMX-HELIXORIENT(1) GROMACS GMX-HELIXORIENT(1) 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 correspond- ing 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 h5md -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 2026, GROMACS development team 2026.3 Jun 25, 2026 GMX-HELIXORIENT(1)
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