NAME

       g_vanhove - calculates Van Hove displacement functions

       VERSION 4.6.5

SYNOPSIS

       g_vanhove  -f  traj.xtc  -s  topol.tpr  -n  index.ndx -om vanhove.xpm -or vanhove_r.xvg -ot vanhove_t.xvg
       -[no]h -[no]version -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

DESCRIPTION

         g_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.   g_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.

FILES

       -f traj.xtc Input
        Trajectory: xtc trr trj gro g96 pdb cpt

       -s topol.tpr Input
        Structure+mass(db): tpr tpb tpa gro g96 pdb

       -n index.ndx Input, Opt.
        Index file

       -om vanhove.xpm Output, Opt.
        X PixMap compatible matrix file

       -or vanhove_r.xvg Output, Opt.
        xvgr/xmgr file

       -ot vanhove_t.xvg Output, Opt.
        xvgr/xmgr file

OTHER OPTIONS

       -[no]hno
        Print help info and quit

       -[no]versionno
        Print version info and quit

       -nice int 19
        Set the nicelevel

       -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]wno
        View output  .xvg,  .xpm,  .eps and  .pdb files

       -xvg enum xmgrace
        xvg plot formatting:  xmgrace,  xmgr or  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

SEE ALSO

       gromacs(7)

       More information about GROMACS is available at <http://www.gromacs.org/>.

                                                 Mon 2 Dec 2013                                     g_vanhove(1)