Provided by: gromacs-data_4.6.5-1build1_all

**NAME**

g_vanhove - calculates Van Hove displacement functionsVERSION4.6.5

**SYNOPSIS**

g_vanhove-ftraj.xtc-stopol.tpr-nindex.ndx-omvanhove.xpm-orvanhove_r.xvg-otvanhove_t.xvg-[no]h-[no]version-niceint-btime-etime-dttime-[no]w-xvgenum-sqrtreal-fmint-rmaxreal-rbinreal-mmaxreal-nlevelsint-nrint-frint-rtreal-ftint

**DESCRIPTION**

g_vanhovecomputes 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_vanhovedetermines 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.

**FILES**

-ftraj.xtcInputTrajectory: xtc trr trj gro g96 pdb cpt-stopol.tprInputStructure+mass(db): tpr tpb tpa gro g96 pdb-nindex.ndxInput,Opt.Index file-omvanhove.xpmOutput,Opt.X PixMap compatible matrix file-orvanhove_r.xvgOutput,Opt.xvgr/xmgr file-otvanhove_t.xvgOutput,Opt.xvgr/xmgr file

**OTHER** **OPTIONS**

-[no]hnoPrint help info and quit-[no]versionnoPrint version info and quit-niceint19Set the nicelevel-btime0First frame (ps) to read from trajectory-etime0Last frame (ps) to read from trajectory-dttime0Only use frame when t MOD dt = first time (ps)-[no]wnoView output.xvg,.xpm,.epsand.pdbfiles-xvgenumxmgracexvg plot formatting:xmgrace,xmgrornone-sqrtreal0Use sqrt(t) on the matrix axis which binspacing in sqrt(ps)-fmint0Number of frames in the matrix, 0 is plot all-rmaxreal2Maximum r in the matrix (nm)-rbinreal0.01Binwidth in the matrix and for-or(nm)-mmaxreal0Maximum density in the matrix, 0 is calculate (1/nm)-nlevelsint81Number of levels in the matrix-nrint1Number of curves for the-oroutput-frint0Frame spacing for the-oroutput-rtreal0Integration limit for the-otoutput (nm)-ftint0Number of frames in the-otoutput, 0 is plot all

**SEE** **ALSO**

gromacs(7)More information aboutGROMACSis available at <http://www.gromacs.org/>. Mon 2 Dec 2013 g_vanhove(1)