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

# gmx-vanhove(1)

Compute Van Hove displacement and correlation functions

## NAME

gmx-vanhove - Compute Van Hove displacement and correlation functions

## SYNOPSIS

```
gmx vanhove [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
            [-om [<.xpm>]] [-or [<.xvg>]] [-ot [<.xvg>]] [-b <time>]
            [-e <time>] [-dt <time>] [-[no]w] [-xvg <enum>]
            [-sqrt <real>] [-fm <int>] [-rmax <real>] [-rbin <real>]
            [-mmax <real>] [-nlevels <int>] [-nr <int>] [-fr <int>]
            [-rt <real>] [-ft <int>]
```

## DESCRIPTION

**gmx vanhove** computes the Van Hove correlation function. The Van Hove G(r,t) is the probability that a particle that is at r\_0 at time zero can be found at position r\_0+r at time t. **gmx vanhove** determines G not for a vector r, but for the length of r. Thus it gives the probability that a particle moves a distance of r in time t. Jumps across the periodic boundaries are removed. Corrections are made for scaling due to isotropic or anisotropic pressure coupling.

With option **-om** the whole matrix can be written as a function of t and r or as a function of sqrt(t) and r (option **-sqrt**).

With option **-or** the Van Hove function is plotted for one or more values of t. Option **-nr** sets the number of times, option **-fr** the number spacing between the times. The binwidth is set with option **-rbin**. The number of bins is determined automatically.

With option **-ot** the integral up to a certain distance (option **-rt**) is plotted as a function of time.

For all frames that are read the coordinates of the selected particles are stored in memory. Therefore the program may use a lot of memory. For options **-om** and **-ot** the program may be slow. This is because the calculation scales as the number of frames times **-fm** or **-ft**. Note that with the **-dt** option the memory usage and calculation time can be reduced.

## 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:

- **-om \[\<.xpm\>\] (vanhove.xpm) (Optional)**

  X PixMap compatible matrix file

- **-or \[\<.xvg\>\] (vanhove\_r.xvg) (Optional)**

  xvgr/xmgr file

- **-ot \[\<.xvg\>\] (vanhove\_t.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)

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

  View output *.xvg*, *.xpm*, *.eps* and *.pdb* files

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

  xvg plot formatting: xmgrace, xmgr, none

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

  Use sqrt(t) on the matrix axis which binspacing # in sqrt(ps)

- **-fm \<int\> (0)**

  Number of frames in the matrix, 0 is plot all

- **-rmax \<real\> (2)**

  Maximum r in the matrix (nm)

- **-rbin \<real\> (0.01)**

  Binwidth in the matrix and for **-or** (nm)

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

  Maximum density in the matrix, 0 is calculate (1/nm)

- **-nlevels \<int\> (81)**

  Number of levels in the matrix

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

  Number of curves for the **-or** output

- **-fr \<int\> (0)**

  Frame spacing for the **-or** output

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

  Integration limit for the **-ot** output (nm)

- **-ft \<int\> (0)**

  Number of frames in the **-ot** output, 0 is plot all

## SEE ALSO

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

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

## COPYRIGHT

2025, GROMACS development team