# gmx-vanhove - Man Page

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/ā¦>] (traj.xtc)**Trajectory: xtc trr cpt gro g96 pdb tng

**-s [<.tpr/.gro/ā¦>] (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

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

## Copyright

2020, GROMACS development team