---
name: "gmx-traj"
section: "1"
platform: "linux"
package: "gromacs-data"
version: "2025.2-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/gmx-traj"
---

# gmx-traj(1)

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

## NAME

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.

See *gmx trajectory* for plotting similar data for selections.

## 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)**

  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

- **-\[no\]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 instead of 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)](/gmx/1.md)**

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

## COPYRIGHT

2025, GROMACS development team