Provided by: gromacs-data_4.6.5-1build1_all bug


       g_vanhove - calculates Van Hove displacement functions

       VERSION 4.6.5


       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


        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


       -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

        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)

        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



       More information about GROMACS is available at <>.

                                          Mon 2 Dec 2013                             g_vanhove(1)