# gmx-vanhove man page

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)**- 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

gmx(1)

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

## Copyright

2016, GROMACS development team