Provided by: gromacs-data_2019.3-2_all bug

NAME

       gmx-vanhove - Compute Van Hove displacement and correlation functions

SYNOPSIS

          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>]

DESCRIPTION

       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

       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)
              Time of first frame to read from trajectory (default unit ps)

       -e <time> (0)
              Time of last frame to read from trajectory (default unit ps)

       -dt <time> (0)
              Only use frame when t MOD dt = first time (default unit 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

SEE ALSO

       gmx(1)

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

COPYRIGHT

       2019, GROMACS development team