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Man Pages


Manual Reference Pages  -  GMX-PRINCIPAL (1)

NAME

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

CONTENTS

Synopsis
Description
Options
See Also

SYNOPSIS

gmx principal [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]]
[-n [<.ndx>]] [-a1 [<.xvg>]] [-a2 [<.xvg>]]
[-a3 [<.xvg>]] [-om [<.xvg>]] [-nice <int>] [-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 and output files:

-f [<.xtc/.trr/...>] (traj.xtc) (Input)
Trajectory: xtc trr cpt trj gro g96 pdb tng

-s [<.tpr/.tpb/...>] (topol.tpr) (Input)
Structure+mass(db): tpr tpb tpa gro g96 pdb brk ent

-n [<.ndx>] (index.ndx) (Input, Optional)
Index file

-a1 [<.xvg>] (paxis1.xvg) (Output)
xvgr/xmgr file

-a2 [<.xvg>] (paxis2.xvg) (Output)
xvgr/xmgr file

-a3 [<.xvg>] (paxis3.xvg) (Output)
xvgr/xmgr file

-om [<.xvg>] (moi.xvg) (Output)
xvgr/xmgr file

Other options:

-nice <int> (19)
Set the nicelevel

-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)
Time unit: 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

gromacs(7)

More information about GROMACS is available at <http://www.gromacs.org/>.

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VERSION 5.0.6 GMX-PRINCIPAL (1)

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