gmx principal

Main Table of Contents VERSION 5.0.5


gmx principal [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]] [-n [<.ndx>]]
             [-a1 [<.xvg>]] [-a2 [<.xvg>]] [-a3 [<.xvg>]] [-om [<.xvg>]]
             [-nice ] [-b 


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 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