Man page - gmx-principal(1)
Packages contains this manual
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- gmx-wheel(1)
- gmx-genion(1)
- gmx-energy(1)
- gmx-rmsdist(1)
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- demux(1)
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- xplor2gmx(1)
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- gmx-rdf(1)
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- gmx-traj(1)
- gmx_mpi_d(1)
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- gmx-nmtraj(1)
apt-get install gromacs-data
Manual
GMX-PRINCIPAL
NAMESYNOPSIS
DESCRIPTION
OPTIONS
SEE ALSO
COPYRIGHT
NAME
gmx-principal - Calculate principal axes of inertia for a group of atoms
SYNOPSIS
gmx principal
[
-f
[<.xtc/.trr/...>]
] [
-s
[<.tpr/.gro/...>]
]
[
-n
[<.ndx>]
] [
-a1
[<.xvg>]
] [
-a2
[<.xvg>]
]
[
-a3
[<.xvg>]
] [
-om
[<.xvg>]
] [
-b
<time>
]
[
-e
<time>
]
[
-dt
<time>
] [
-tu
<enum>
] [
-[no]w
] [
-xvg
<enum>
]
[
-[no]foo
]
DESCRIPTION
gmx principal calculates the three principal axes of inertia for a group of atoms. NOTE: Old versions of GROMACS wrote the output data in a strange transposed way. As of GROMACS 5.0, the output file paxis1.dat contains the x/y/z components of the first (major) principal axis for each frame, and similarly for the middle and minor axes in paxis2.dat and paxis3.dat.
OPTIONS
Options to
specify input files:
-f [<.xtc/.trr/...>] (traj.xtc)
Trajectory: xtc trr cpt gro g96 pdb tng
-s [<.tpr/.gro/...>] (topol.tpr)
Structure+mass(db): tpr gro g96 pdb brk ent
-n [<.ndx>] (index.ndx) (Optional)
Index file
Options to
specify output files:
-a1 [<.xvg>] (paxis1.xvg)
xvgr/xmgr file
-a2 [<.xvg>] (paxis2.xvg)
xvgr/xmgr file
-a3 [<.xvg>] (paxis3.xvg)
xvgr/xmgr file
-om [<.xvg>] (moi.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)
-tu <enum> (ps)
Unit for time values: fs, ps, ns, us, ms, s
-[no]w (no)
View output .xvg , .xpm , .eps and .pdb files
-xvg <enum> (xmgrace)
xvg plot formatting: xmgrace, xmgr, none
-[no]foo (no)
Dummy option to avoid empty array
SEE ALSO
gmx(1)
More information about GROMACS is available at <- http://www.gromacs.org/ >.
COPYRIGHT
2025, GROMACS development team