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

# gmx-distance(1)

Calculate distances between pairs of positions

## NAME

gmx-distance - Calculate distances between pairs of positions

## SYNOPSIS

```
gmx distance [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
             [-oav [<.xvg>]] [-oall [<.xvg>]] [-oxyz [<.xvg>]]
             [-oh [<.xvg>]] [-oallstat [<.xvg>]] [-b <time>]
             [-e <time>] [-dt <time>] [-tu <enum>]
             [-fgroup <selection>] [-xvg <enum>] [-[no]rmpbc]
             [-[no]pbc] [-sf <file>] [-selrpos <enum>]
             [-seltype <enum>] [-select <selection>] [-len <real>]
             [-tol <real>] [-binw <real>]
```

## DESCRIPTION

**gmx distance** calculates distances between pairs of positions as a function of time. Each selection specifies an independent set of distances to calculate. Each selection should consist of pairs of positions, and the distances are computed between positions 1-2, 3-4, etc.

**-oav** writes the average distance as a function of time for each selection. **-oall** writes all the individual distances. **-oxyz** does the same, but the x, y, and z components of the distance are written instead of the norm. **-oh** writes a histogram of the distances for each selection. The location of the histogram is set with **-len** and **-tol**. Bin width is set with **-binw**. **-oallstat** writes out the average and standard deviation for each individual distance, calculated over the frames.

Note that **gmx distance** calculates distances between fixed pairs (1-2, 3-4, etc.) within a single selection.  To calculate distances between two selections, including minimum, maximum, and pairwise distances, use *gmx pairdist*.

## OPTIONS

Options to specify input files:

- **-f \[\<.xtc/.trr/...\>\] (traj.xtc) (Optional)**

  Input trajectory or single configuration: *xtc* *trr* *cpt* *gro* *g96* *pdb* *tng*

- **-s \[\<.tpr/.gro/...\>\] (topol.tpr) (Optional)**

  Input structure: *tpr* *gro* *g96* *pdb* brk ent

- **-n \[\<.ndx\>\] (index.ndx) (Optional)**

  Extra index groups

Options to specify output files:

- **-oav \[\<.xvg\>\] (distave.xvg) (Optional)**

  Average distances as function of time

- **-oall \[\<.xvg\>\] (dist.xvg) (Optional)**

  All distances as function of time

- **-oxyz \[\<.xvg\>\] (distxyz.xvg) (Optional)**

  Distance components as function of time

- **-oh \[\<.xvg\>\] (disthist.xvg) (Optional)**

  Histogram of the distances

- **-oallstat \[\<.xvg\>\] (diststat.xvg) (Optional)**

  Statistics for individual distances

Other options:

- **-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 if t MOD dt == first time (ps)

- **-tu \<enum\> (ps)**

  Unit for time values: fs, ps, ns, us, ms, s

- **-fgroup \<selection\>**

  Atoms stored in the trajectory file (if not set, assume first N atoms)

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

  Plot formatting: xmgrace, xmgr, none

- **-\[no\]rmpbc (yes)**

  Make molecules whole for each frame

- **-\[no\]pbc (yes)**

  Use periodic boundary conditions for distance calculation

- **-sf \<file\>**

  Provide selections from files

- **-selrpos \<enum\> (atom)**

  Selection reference positions: atom, res\_com, res\_cog, mol\_com, mol\_cog, whole\_res\_com, whole\_res\_cog, whole\_mol\_com, whole\_mol\_cog, part\_res\_com, part\_res\_cog, part\_mol\_com, part\_mol\_cog, dyn\_res\_com, dyn\_res\_cog, dyn\_mol\_com, dyn\_mol\_cog

- **-seltype \<enum\> (atom)**

  Default selection output positions: atom, res\_com, res\_cog, mol\_com, mol\_cog, whole\_res\_com, whole\_res\_cog, whole\_mol\_com, whole\_mol\_cog, part\_res\_com, part\_res\_cog, part\_mol\_com, part\_mol\_cog, dyn\_res\_com, dyn\_res\_cog, dyn\_mol\_com, dyn\_mol\_cog

- **-select \<selection\>**

  Position pairs to calculate distances for

- **-len \<real\> (0.1)**

  Mean distance for histogramming

- **-tol \<real\> (1)**

  Width of full distribution as fraction of **-len**

- **-binw \<real\> (0.001)**

  Bin width for histogramming

## SEE ALSO

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

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

## COPYRIGHT

2025, GROMACS development team