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gmx-principal - Calculate principal axes of inertia for a group of atoms

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

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)
First frame (ps) to read from trajectory
-e <time> (0)
Last frame (ps) to read from trajectory
-dt <time> (0)
Only use frame when t MOD dt = first time (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/>. 2017, GROMACS development team
September 15, 2017 2016.4