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g_vanhoveMain Table of Contents |
VERSION 4.6.3
Fri 5 Jul 2013
| VERSION 4.6.3 |
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 |