---
name: "g_traj"
section: "1"
platform: "linux"
package: "gromacs-data"
version: "5.0.2-1"
release: "Debian 8 (Jessie)"
platforms: ["linux"]
url: "https://new.carta.tech/gmx-traj"
---

# g\_traj(1)

Plot x, v, f, box, temperature and rotational energy from trajectories

Part of [gmx-traj(1)](/gmx-traj/1.md).

## NAME

gmx-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 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 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 ALSO

**[gromacs(7)](/gromacs/7.md)**

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