gmx-vanhove (1)

gmx vanhove [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]]

            [-n [<.ndx>]] [-om [<.xpm>]] [-or [<.xvg>]]
            [-ot [<.xvg>]] [-nice <int>] [-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 and output files:

-f [<.xtc/.trr/...>] (traj.xtc) (Input)

    Trajectory: xtc trr cpt trj gro g96 pdb tng

-s [<.tpr/.tpb/...>] (topol.tpr) (Input)

    Structure+mass(db): tpr tpb tpa gro g96 pdb brk ent

-n [<.ndx>] (index.ndx) (Input, Optional)

    Index file

-om [<.xpm>] (vanhove.xpm) (Output, Optional)

    X PixMap compatible matrix file

-or [<.xvg>] (vanhove_r.xvg) (Output, Optional)

    xvgr/xmgr file

-ot [<.xvg>] (vanhove_t.xvg) (Output, Optional)

    xvgr/xmgr file

Other options:

-nice <int> (19)

    Set the nicelevel

-b <time> (0)

    First frame (ps) to read from trajectory

-e <time> (0)

    Last frame (ps) to read from trajectory

-dt <time> (0)

    Only use frame when t MOD dt = first time (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

gromacs(7)

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