.TH gmx-vanhove 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
gmx-vanhove \- Compute Van Hove displacement and correlation functions

.SH SYNOPSIS
gmx vanhove [\-f [<.xtc/.trr/...>]] [\-s [<.tpr/.tpb/...>]]
            [\-n [<.ndx>]] [\-om [<.xpm>]] [\-or [<.xvg>]]
            [\-ot [<.xvg>]] [\-nice <int>] [\-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>]

.SH DESCRIPTION
\fBgmx vanhove\fR 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. \fBgmx vanhove\fR 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 \fB\-om\fR the whole matrix can be written as a function of t and r or as a function of sqrt(t) and r (option \fB\-sqrt\fR).

With option \fB\-or\fR the Van Hove function is plotted for one or more values of t. Option \fB\-nr\fR sets the number of times, option \fB\-fr\fR the number spacing between the times. The binwidth is set with option \fB\-rbin\fR. The number of bins is determined automatically.

With option \fB\-ot\fR the integral up to a certain distance (option \fB\-rt\fR) 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 \fB\-om\fR and \fB\-ot\fR the program may be slow. This is because the calculation scales as the number of frames times \fB\-fm\fR or \fB\-ft\fR. Note that with the \fB\-dt\fR option the memory usage and calculation time can be reduced.

.SH OPTIONS
Options to specify input and output files:

.BI "\-f" " [<.xtc/.trr/...>] (traj.xtc) (Input)"
    Trajectory: xtc trr cpt trj gro g96 pdb tng

.BI "\-s" " [<.tpr/.tpb/...>] (topol.tpr) (Input)"
    Structure+mass(db): tpr tpb tpa gro g96 pdb brk ent

.BI "\-n" " [<.ndx>] (index.ndx) (Input, Optional)"
    Index file

.BI "\-om" " [<.xpm>] (vanhove.xpm) (Output, Optional)"
    X PixMap compatible matrix file

.BI "\-or" " [<.xvg>] (vanhove_r.xvg) (Output, Optional)"
    xvgr/xmgr file

.BI "\-ot" " [<.xvg>] (vanhove_t.xvg) (Output, Optional)"
    xvgr/xmgr file


Other options:

.BI "\-nice" " <int> (19)"
    Set the nicelevel

.BI "\-b" " <time> (0)"
    First frame (ps) to read from trajectory

.BI "\-e" " <time> (0)"
    Last frame (ps) to read from trajectory

.BI "\-dt" " <time> (0)"
    Only use frame when t MOD dt = first time (ps)

.BI "\-[no]w" "  (no)"
    View output \fB.xvg\fR, \fB.xpm\fR, \fB.eps\fR and \fB.pdb\fR files

.BI "\-xvg" " <enum> (xmgrace)"
    xvg plot formatting: xmgrace, xmgr, none

.BI "\-sqrt" " <real> (0)"
    Use sqrt(t) on the matrix axis which binspacing  in sqrt(ps)

.BI "\-fm" " <int> (0)"
    Number of frames in the matrix, 0 is plot all

.BI "\-rmax" " <real> (2)"
    Maximum r in the matrix (nm)

.BI "\-rbin" " <real> (0.01)"
    Binwidth in the matrix and for \fB\-or\fR (nm)

.BI "\-mmax" " <real> (0)"
    Maximum density in the matrix, 0 is calculate (1/nm)

.BI "\-nlevels" " <int> (81)"
    Number of levels in the matrix

.BI "\-nr" " <int> (1)"
    Number of curves for the \fB\-or\fR output

.BI "\-fr" " <int> (0)"
    Frame spacing for the \fB\-or\fR output

.BI "\-rt" " <real> (0)"
    Integration limit for the \fB\-ot\fR output (nm)

.BI "\-ft" " <int> (0)"
    Number of frames in the \fB\-ot\fR output, 0 is plot all


.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.