| VERSION 4.6.1 |
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.
option | filename | type | description |
---|---|---|---|
-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 |
option | type | default | description |
---|---|---|---|
-[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 |