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

# g\_vanhove\_d(1)

Compute Van Hove displacement and correlation functions

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

## NAME

gmx-vanhove - Compute Van Hove displacement and correlation functions

## SYNOPSIS

gmx vanhove \[-f \[\<.xtc/.trr/...\>\]\] \[-s \[\<.tpr/.tpb/...\>\]\]\
             \[-n \[\<.ndx\>\]\] \[-om \[\<.xpm\>\]\] \[-or \[\<.xvg\>\]\]\
             \[-ot \[\<.xvg\>\]\] \[-nice \<int\>\] \[-b \<time\>\] \[-e \<time\>\]\
             \[-dt \<time\>\] \[-\[no\]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 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

**-om** *\[\<.xpm\>\] (vanhove.xpm) (Output, Optional)*\
     X PixMap compatible matrix file

**-or** *\[\<.xvg\>\] (vanhove\_r.xvg) (Output, Optional)*\
     xvgr/xmgr file

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

**-\[no\]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

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

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