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

# trjorder(1)

Order molecules according to their distance to a group

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

## NAME

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

## SYNOPSIS

gmx trjorder \[-f \[\<.xtc/.trr/...\>\]\] \[-s \[\<.tpr/.tpb/...\>\]\]\
              \[-n \[\<.ndx\>\]\] \[-o \[\<.xtc/.trr/...\>\]\] \[-nshell \[\<.xvg\>\]\]\
              \[-nice \<int\>\] \[-b \<time\>\] \[-e \<time\>\] \[-dt \<time\>\]\
              \[-xvg \<enum\>\] \[-na \<int\>\] \[-da \<int\>\] \[-\[no\]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 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

**-o** *\[\<.xtc/.trr/...\>\] (ordered.xtc) (Output, Optional)*\
     Trajectory: xtc trr trj gro g96 pdb tng

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

**-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

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

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