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

# gmx-trjorder(1)

Order molecules according to their distance to a group

## NAME

gmx-trjorder - Order molecules according to their distance to a group

## SYNOPSIS

```
gmx trjorder [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
             [-o [<.xtc/.trr/...>]] [-nshell [<.xvg>]] [-b <time>]
             [-e <time>] [-dt <time>] [-xvg <enum>] [-na <int>]
             [-da <int>] [-[no]com] [-r <real>] [-[no]z]
```

## DESCRIPTION

**gmx trjorder** orders molecules according to the smallest distance to atoms in a reference group or on z-coordinate (with option **-z**). With distance ordering, it will ask for a group of reference atoms and a group of molecules. For each frame of the trajectory the selected molecules will be reordered according to the shortest distance between atom number **-da** in the molecule and all the atoms in the reference group. The center of mass of the molecules can be used instead of a reference atom by setting **-da** to 0. All atoms in the trajectory are written to the output trajectory.

**gmx trjorder** can be useful for e.g. analyzing the n waters closest to a protein. In that case the reference group would be the protein and the group of molecules would consist of all the water atoms. When an index group of the first n waters is made, the ordered trajectory can be used with any GROMACS program to analyze the n closest waters.

If the output file is a *.pdb* file, the distance to the reference target will be stored in the B-factor field in order to color with e.g. Rasmol.

With option **-nshell** the number of molecules within a shell of radius **-r** around the reference group are printed.

## 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:

- **-o \[\<.xtc/.trr/...\>\] (ordered.xtc) (Optional)**

  Trajectory: *xtc* *trr* *gro* *g96* *pdb* *tng*

- **-nshell \[\<.xvg\>\] (nshell.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)

- **-xvg \<enum\> (xmgrace)**

  xvg plot formatting: xmgrace, xmgr, none

- **-na \<int\> (3)**

  Number of atoms in a molecule

- **-da \<int\> (1)**

  Atom used for the distance calculation, 0 is COM

- **-\[no\]com (no)**

  Use the distance to the center of mass of the reference group

- **-r \<real\> (0)**

  Cutoff used for the distance calculation when computing the number of molecules in a shell around e.g. a protein

- **-\[no\]z (no)**

  Order molecules on z-coordinate

## SEE ALSO

**[gmx(1)](/gmx/1.md)**

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

## COPYRIGHT

2025, GROMACS development team