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       g_vanhove - calculates Van Hove displacement functions

       VERSION 4.0.1


       g_vanhove  -f  traj.xtc  -s  topol.tpr -n index.ndx -om vanhove.xpm -or
       vanhove_r.xvg -ot vanhove_t.xvg -[no]h -nice int -b time  -e  time  -dt
       time  -[no]w  -[no]xvgr  -sqrt real -fm int -rmax real -rbin real -mmax
       real -nlevels int -nr int -fr int -rt real -ft int


       g_vanhove computes the Van Hove correlation  function.   The  Van  Hove
       G(r,t)  is  the  probability that a particle that is at r0 at time zero
       can be found at position r0+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


       -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


        Print help 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)

        View output xvg, xpm, eps and pdb files

        Add specific codes (legends etc.) in the  output  xvg  files  for  the
       xmgrace program

       -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



       More      information     about     GROMACS     is     available     at

                                Thu 16 Oct 2008                   g_vanhove(1)