gmx-vanhove - Compute Van Hove displacement and correlation functions

       2025, GROMACS development team

2025.0                                            Feb 10, 2025                                    GMX-VANHOVE(1)

gmxvanhove  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.  gmxvanhove 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.

       gmx-vanhove - Compute Van Hove displacement and correlation functions

       Options to specify input files:

       -f[<.xtc/.trr/...>](traj.xtc)
              Trajectory: xtctrrcptgrog96pdbtng-s[<.tpr/.gro/...>](topol.tpr)
              Structure+mass(db): tprgrog96pdb 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

gmx(1)

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

          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>]