.TH gmx-principal 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
gmx-principal \- Calculate principal axes of inertia for a group of atoms

.SH 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]

.SH DESCRIPTION
\fBgmx principal\fR 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.

.SH OPTIONS
Options to specify input and output files:

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

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

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

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

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

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

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


Other options:

.BI "\-nice" " <int> (19)"
    Set the nicelevel

.BI "\-b" " <time> (0)"
    First frame (ps) to read from trajectory

.BI "\-e" " <time> (0)"
    Last frame (ps) to read from trajectory

.BI "\-dt" " <time> (0)"
    Only use frame when t MOD dt = first time (ps)

.BI "\-tu" " <enum> (ps)"
    Time unit: fs, ps, ns, us, ms, s

.BI "\-[no]w" "  (no)"
    View output \fB.xvg\fR, \fB.xpm\fR, \fB.eps\fR and \fB.pdb\fR files

.BI "\-xvg" " <enum> (xmgrace)"
    xvg plot formatting: xmgrace, xmgr, none

.BI "\-[no]foo" "  (no)"
    Dummy option to avoid empty array


.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.