# 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)- 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>- 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