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
More information about GROMACS is available at <- http://www.gromacs.org/>.
COPYRIGHT
2020, GROMACS development team