gmx-principal1
Calculate principal axes of inertia for a group of atoms
Usage
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]
Overview
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 |
Releases
6 releases since Debian 8 (Jessie); the text changed 5 times.