gmx-traj(1) GROMACS Manual gmx-traj(1)NAMEgmx-traj - Plot x, v, f, box, temperature and rotational energy from
trajectories
SYNOPSIS
gmx traj [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]] [-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>]] [-nice <int>] [-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 cen‐
ter 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 vec‐
tor is plotted. In addition in the same graph the kinetic energy dis‐
tribution is given.
OPTIONS
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
-ox [<.xvg>] (coord.xvg) (Output, Optional)
xvgr/xmgr file
-oxt [<.xtc/.trr/...>] (coord.xtc) (Output, Optional)
Trajectory: xtc trr cpt trj gro g96 pdb tng
-ov [<.xvg>] (veloc.xvg) (Output, Optional)
xvgr/xmgr file
-of [<.xvg>] (force.xvg) (Output, Optional)
xvgr/xmgr file
-ob [<.xvg>] (box.xvg) (Output, Optional)
xvgr/xmgr file
-ot [<.xvg>] (temp.xvg) (Output, Optional)
xvgr/xmgr file
-ekt [<.xvg>] (ektrans.xvg) (Output, Optional)
xvgr/xmgr file
-ekr [<.xvg>] (ekrot.xvg) (Output, Optional)
xvgr/xmgr file
-vd [<.xvg>] (veldist.xvg) (Output, Optional)
xvgr/xmgr file
-cv [<.pdb>] (veloc.pdb) (Output, Optional)
Protein data bank file
-cf [<.pdb>] (force.pdb) (Output, Optional)
Protein data bank file
-av [<.xvg>] (all_veloc.xvg) (Output, Optional)
xvgr/xmgr file
-af [<.xvg>] (all_force.xvg) (Output, Optional)
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]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 ALSOgromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6gmx-traj(1)
