gmx vanhove#

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): 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