Provided by: gromacs-data_2019.3-2_all

**NAME**

gmx-vanhove - Compute Van Hove displacement and correlation functions

**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**

gmxvanhovecomputes 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.gmxvanhovedetermines 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-omthe 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-orthe Van Hove function is plotted for one or more values of t. Option-nrsets the number of times, option-frthe number spacing between the times. The binwidth is set with option-rbin. The number of bins is determined automatically. With option-otthe 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-omand-otthe program may be slow. This is because the calculation scales as the number of frames times-fmor-ft. Note that with the-dtoption 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-oroutput-fr<int>(0)Frame spacing for the-oroutput-rt<real>(0)Integration limit for the-otoutput (nm)-ft<int>(0)Number of frames in the-otoutput, 0 is plot all

**SEE** **ALSO**

gmx(1)More information about GROMACS is available at <http://www.gromacs.org/>.

**COPYRIGHT**

2019, GROMACS development team