1GMX-HELIXORIENT(1)                  GROMACS                 GMX-HELIXORIENT(1)
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NAME

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

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

18       gmx helixorient calculates the coordinates and direction of the average
19       axis  inside an alpha helix, and the direction/vectors of both the Cal‐
20       pha and (optionally) a sidechain atom relative to the axis.
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22       As input, you need to specify an index group with Calpha  atoms  corre‐
23       sponding to an alpha-helix of continuous residues. Sidechain directions
24       require a second index group of the same  size,  containing  the  heavy
25       atom in each residue that should represent the sidechain.
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27       Note that this program does not do any fitting of structures.
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29       We  need  four  Calpha coordinates to define the local direction of the
30       helix axis.
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32       The tilt/rotation is calculated from Euler rotations, where  we  define
33       the  helix  axis  as the local x-axis, the residues/Calpha vector as y,
34       and the z-axis from their cross product. We use the Euler  Y-Z-X  rota‐
35       tion,  meaning we first tilt the helix axis (1) around and (2) orthogo‐
36       nal to the residues vector, and finally apply the (3)  rotation  around
37       it. For debugging or other purposes, we also write out the actual Euler
38       rotation angles as theta[1-3].xvg
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OPTIONS

41       Options to specify input files:
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43       -s [<.tpr>] (topol.tpr)
44              Portable xdr run input file
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46       -f [<.xtc/.trr/…>] (traj.xtc)
47              Trajectory: xtc trr cpt gro g96 pdb tng
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49       -n [<.ndx>] (index.ndx) (Optional)
50              Index file
51
52       Options to specify output files:
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54       -oaxis [<.dat>] (helixaxis.dat)
55              Generic data file
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57       -ocenter [<.dat>] (center.dat)
58              Generic data file
59
60       -orise [<.xvg>] (rise.xvg)
61              xvgr/xmgr file
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63       -oradius [<.xvg>] (radius.xvg)
64              xvgr/xmgr file
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66       -otwist [<.xvg>] (twist.xvg)
67              xvgr/xmgr file
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69       -obending [<.xvg>] (bending.xvg)
70              xvgr/xmgr file
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72       -otilt [<.xvg>] (tilt.xvg)
73              xvgr/xmgr file
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75       -orot [<.xvg>] (rotation.xvg)
76              xvgr/xmgr file
77
78       Other options:
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80       -b <time> (0)
81              Time of first frame to read from trajectory (default unit ps)
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83       -e <time> (0)
84              Time of last frame to read from trajectory (default unit ps)
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86       -dt <time> (0)
87              Only use frame when t MOD dt = first time (default unit ps)
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89       -xvg <enum> (xmgrace)
90              xvg plot formatting: xmgrace, xmgr, none
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92       -[no]sidechain (no)
93              Calculate sidechain directions relative to helix axis too.
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95       -[no]incremental (no)
96              Calculate incremental rather than total rotation/tilt.
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SEE ALSO

99       gmx(1)
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101       More    information    about    GROMACS    is    available    at     <‐
102       http://www.gromacs.org/>.
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105       2020, GROMACS development team
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1102019.6                           Feb 28, 2020               GMX-HELIXORIENT(1)
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