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GMX-VANHOVE(1) GROMACS GMX-VANHOVE(1)

gmx-vanhove - Compute Van Hove displacement and correlation functions

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>]


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 to specify input files:

Trajectory: xtc trr cpt gro g96 pdb tng
Structure+mass(db): tpr gro g96 pdb brk ent
Index file

Options to specify output files:

X PixMap compatible matrix file
xvgr/xmgr file
xvgr/xmgr file

Other options:

Time of first frame to read from trajectory (default unit ps)
Time of last frame to read from trajectory (default unit ps)
Only use frame when t MOD dt = first time (default unit ps)
-[no]w (no)
View output .xvg, .xpm, .eps and .pdb files
xvg plot formatting: xmgrace, xmgr, none
Use sqrt(t) on the matrix axis which binspacing # in sqrt(ps)
Number of frames in the matrix, 0 is plot all
Maximum r in the matrix (nm)
Binwidth in the matrix and for -or (nm)
Maximum density in the matrix, 0 is calculate (1/nm)
Number of levels in the matrix
Number of curves for the -or output
Frame spacing for the -or output
Integration limit for the -ot output (nm)
Number of frames in the -ot output, 0 is plot all

gmx(1)

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2021, GROMACS development team

March 29, 2021 2020.6-Debian-2020.6-2