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g_vanhove - calculates Van Hove displacement functionsVERSION4.0.1

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

g_vanhove computes the Van Hove correlation function. The Van Hove G(r,t) is the probability that a particle that is at r0 at time zero can be found at position r0+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-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.

-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

-[no]hnoPrint help 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, eps and pdb files-[no]xvgryesAdd specific codes (legends etc.) in the output xvg files for the xmgrace program-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 -or output-frint0Frame spacing for the -or output-rtreal0Integration limit for the -ot output (nm)-ftint0Number of frames in the -ot output, 0 is plot all

gromacs(7)More information aboutGROMACSis available at <http://www.gromacs.org/>. Thu 16 Oct 2008 g_vanhove(1)