gmx-vanhove - Compute Van Hove displacement and correlation functions

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>*]

**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 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

**gmx(1)**

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2017, GROMACS development team