xenial (1) gmx-vanhove.1.gz

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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)
              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]w (no)
              View output .xvg, .xpm, .eps and .pdb files

       -xvg <enum>
              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/>.

       2015, GROMACS development team