Main Table of Contents

Wed 13 Nov 2013


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 reduced.


-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

Other options

-[no]h bool no Print help info and quit
-[no]version bool no 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)
-[no]w bool no 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