1GMX-PRINCIPAL(1)                    GROMACS                   GMX-PRINCIPAL(1)
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NAME

6       gmx-principal  -  Calculate  principal  axes  of inertia for a group of
7       atoms
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SYNOPSIS

10          gmx principal [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]]
11                       [-n [<.ndx>]] [-a1 [<.xvg>]] [-a2 [<.xvg>]]
12                       [-a3 [<.xvg>]] [-om [<.xvg>]] [-b <time>] [-e <time>]
13                       [-dt <time>] [-tu <enum>] [-[no]w] [-xvg <enum>]
14                       [-[no]foo]
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DESCRIPTION

17       gmx principal calculates the three principal  axes  of  inertia  for  a
18       group  of atoms. NOTE: Old versions of GROMACS wrote the output data in
19       a strange transposed way. As of GROMACS 5.0, the output file paxis1.dat
20       contains  the  x/y/z components of the first (major) principal axis for
21       each frame, and similarly for the middle and minor axes  in  paxis2.dat
22       and paxis3.dat.
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OPTIONS

25       Options to specify input files:
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27       -f [<.xtc/.trr/…>] (traj.xtc)
28              Trajectory: xtc trr cpt gro g96 pdb tng
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30       -s [<.tpr/.gro/…>] (topol.tpr)
31              Structure+mass(db): tpr gro g96 pdb brk ent
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33       -n [<.ndx>] (index.ndx) (Optional)
34              Index file
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36       Options to specify output files:
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38       -a1 [<.xvg>] (paxis1.xvg)
39              xvgr/xmgr file
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41       -a2 [<.xvg>] (paxis2.xvg)
42              xvgr/xmgr file
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44       -a3 [<.xvg>] (paxis3.xvg)
45              xvgr/xmgr file
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47       -om [<.xvg>] (moi.xvg)
48              xvgr/xmgr file
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50       Other options:
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52       -b <time> (0)
53              Time of first frame to read from trajectory (default unit ps)
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55       -e <time> (0)
56              Time of last frame to read from trajectory (default unit ps)
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58       -dt <time> (0)
59              Only use frame when t MOD dt = first time (default unit ps)
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61       -tu <enum> (ps)
62              Unit for time values: fs, ps, ns, us, ms, s
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64       -[no]w (no)
65              View output .xvg, .xpm, .eps and .pdb files
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67       -xvg <enum> (xmgrace)
68              xvg plot formatting: xmgrace, xmgr, none
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70       -[no]foo (no)
71              Dummy option to avoid empty array
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SEE ALSO

74       gmx(1)
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76       More     information    about    GROMACS    is    available    at    <‐
77       http://www.gromacs.org/>.
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80       2020, GROMACS development team
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852019.6                           Feb 28, 2020                 GMX-PRINCIPAL(1)
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