gmx principal¶
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