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gmx-principal - Online in the Cloud

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This is the command gmx-principal that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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>
xvg plot formatting: xmgrace, xmgr, none

-[no]foo (no)
Dummy option to avoid empty array

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