gmx-traj man page

gmx-traj — Plot x, v, f, box, temperature and rotational energy from trajectories

Synopsis

gmx traj [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
         [-ox [<.xvg>]] [-oxt [<.xtc/.trr/...>]] [-ov [<.xvg>]]
         [-of [<.xvg>]] [-ob [<.xvg>]] [-ot [<.xvg>]] [-ekt [<.xvg>]]
         [-ekr [<.xvg>]] [-vd [<.xvg>]] [-cv [<.pdb>]] [-cf [<.pdb>]]
         [-av [<.xvg>]] [-af [<.xvg>]] [-b <time>] [-e <time>]
         [-dt <time>] [-tu <enum>] [-[no]w] [-xvg <enum>] [-[no]com]
         [-[no]pbc] [-[no]mol] [-[no]nojump] [-[no]x] [-[no]y]
         [-[no]z] [-ng <int>] [-[no]len] [-[no]fp] [-bin <real>]
         [-ctime <real>] [-scale <real>]

Description

gmx traj plots coordinates, velocities, forces and/or the box. With -com the coordinates, velocities and forces are calculated for the center of mass of each group. When -mol is set, the numbers in the index file are interpreted as molecule numbers and the same procedure as with -com is used for each molecule.

Option -ot plots the temperature of each group, provided velocities are present in the trajectory file. No corrections are made for constrained degrees of freedom! This implies -com.

Options -ekt and -ekr plot the translational and rotational kinetic energy of each group, provided velocities are present in the trajectory file. This implies -com.

Options -cv and -cf write the average velocities and average forces as temperature factors to a .pdb file with the average coordinates or the coordinates at -ctime. The temperature factors are scaled such that the maximum is 10. The scaling can be changed with the option -scale. To get the velocities or forces of one frame set both -b and -e to the time of desired frame. When averaging over frames you might need to use the -nojump option to obtain the correct average coordinates. If you select either of these option the average force and velocity for each atom are written to an .xvg file as well (specified with -av or -af).

Option -vd computes a velocity distribution, i.e. the norm of the vector is plotted. In addition in the same graph the kinetic energy distribution is given.

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:

-ox [<.xvg>] (coord.xvg) (Optional)
xvgr/xmgr file
-oxt [<.xtc/.trr/...>] (coord.xtc) (Optional)
Trajectory: xtc trr cpt gro g96 pdb tng
-ov [<.xvg>] (veloc.xvg) (Optional)
xvgr/xmgr file
-of [<.xvg>] (force.xvg) (Optional)
xvgr/xmgr file
-ob [<.xvg>] (box.xvg) (Optional)
xvgr/xmgr file
-ot [<.xvg>] (temp.xvg) (Optional)
xvgr/xmgr file
-ekt [<.xvg>] (ektrans.xvg) (Optional)
xvgr/xmgr file
-ekr [<.xvg>] (ekrot.xvg) (Optional)
xvgr/xmgr file
-vd [<.xvg>] (veldist.xvg) (Optional)
xvgr/xmgr file
-cv [<.pdb>] (veloc.pdb) (Optional)
Protein data bank file
-cf [<.pdb>] (force.pdb) (Optional)
Protein data bank file
-av [<.xvg>] (all_veloc.xvg) (Optional)
xvgr/xmgr file
-af [<.xvg>] (all_force.xvg) (Optional)
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> (xmgrace)
xvg plot formatting: xmgrace, xmgr, none
-[no]com (no)
Plot data for the com of each group
-[no]pbc (yes)
Make molecules whole for COM
-[no]mol (no)
Index contains molecule numbers iso atom numbers
-[no]nojump (no)
Remove jumps of atoms across the box
-[no]x (yes)
Plot X-component
-[no]y (yes)
Plot Y-component
-[no]z (yes)
Plot Z-component
-ng <int> (1)
Number of groups to consider
-[no]len (no)
Plot vector length
-[no]fp (no)
Full precision output
-bin <real> (1)
Binwidth for velocity histogram (nm/ps)
-ctime <real> (-1)
Use frame at this time for x in -cv and -cf instead of the average x
-scale <real> (0)
Scale factor for .pdb output, 0 is autoscale

See Also

gmx(1)

More information about GROMACS is available at <http://www.gromacs.org/>.

Referenced By

gmx(1).

Oct 28, 2016 2016.1 GROMACS