# gmx vanhove¶

## 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