Provided by: gromacs-data_2020-2build1_all #### NAME

```       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)
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

```

#### SEEALSO

```       gmx(1)

```       2020, GROMACS development team