1GMX-VANHOVE(1) GROMACS GMX-VANHOVE(1)
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6 gmx-vanhove - Compute Van Hove displacement and correlation functions
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9 gmx vanhove [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
10 [-om [<.xpm>]] [-or [<.xvg>]] [-ot [<.xvg>]] [-b <time>]
11 [-e <time>] [-dt <time>] [-[no]w] [-xvg <enum>]
12 [-sqrt <real>] [-fm <int>] [-rmax <real>] [-rbin <real>]
13 [-mmax <real>] [-nlevels <int>] [-nr <int>] [-fr <int>]
14 [-rt <real>] [-ft <int>]
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17 gmx vanhove computes the Van Hove correlation function. The Van Hove
18 G(r,t) is the probability that a particle that is at r_0 at time zero
19 can be found at position r_0+r at time t. gmx vanhove determines G not
20 for a vector r, but for the length of r. Thus it gives the probability
21 that a particle moves a distance of r in time t. Jumps across the
22 periodic boundaries are removed. Corrections are made for scaling due
23 to isotropic or anisotropic pressure coupling.
24 With option -om the whole matrix can be written as a function of t and
26 r or as a function of sqrt(t) and r (option -sqrt).
27 With option -or the Van Hove function is plotted for one or more values
29 of t. Option -nr sets the number of times, option -fr the number spac‐
30 ing between the times. The binwidth is set with option -rbin. The num‐
31 ber of bins is determined automatically.
32 With option -ot the integral up to a certain distance (option -rt) is
34 plotted as a function of time.
35 For all frames that are read the coordinates of the selected particles
37 are stored in memory. Therefore the program may use a lot of memory.
38 For options -om and -ot the program may be slow. This is because the
39 calculation scales as the number of frames times -fm or -ft. Note that
40 with the -dt option the memory usage and calculation time can be
41 reduced.
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44 Options to specify input files:
45 -f [<.xtc/.trr/…>] (traj.xtc)
47 Trajectory: xtc trr cpt gro g96 pdb tng
48 -s [<.tpr/.gro/…>] (topol.tpr)
50 Structure+mass(db): tpr gro g96 pdb brk ent
51 -n [<.ndx>] (index.ndx) (Optional)
53 Index file
54 Options to specify output files:
56 -om [<.xpm>] (vanhove.xpm) (Optional)
58 X PixMap compatible matrix file
59 -or [<.xvg>] (vanhove_r.xvg) (Optional)
61 xvgr/xmgr file
62 -ot [<.xvg>] (vanhove_t.xvg) (Optional)
64 xvgr/xmgr file
65 Other options:
67 -b <time> (0)
69 Time of first frame to read from trajectory (default unit ps)
70 -e <time> (0)
72 Time of last frame to read from trajectory (default unit ps)
73 -dt <time> (0)
75 Only use frame when t MOD dt = first time (default unit ps)
76 -[no]w (no)
78 View output .xvg, .xpm, .eps and .pdb files
79 -xvg <enum> (xmgrace)
81 xvg plot formatting: xmgrace, xmgr, none
82 -sqrt <real> (0)
84 Use sqrt(t) on the matrix axis which binspacing # in sqrt(ps)
85 -fm <int> (0)
87 Number of frames in the matrix, 0 is plot all
88 -rmax <real> (2)
90 Maximum r in the matrix (nm)
91 -rbin <real> (0.01)
93 Binwidth in the matrix and for -or (nm)
94 -mmax <real> (0)
96 Maximum density in the matrix, 0 is calculate (1/nm)
97 -nlevels <int> (81)
99 Number of levels in the matrix
100 -nr <int> (1)
102 Number of curves for the -or output
103 -fr <int> (0)
105 Frame spacing for the -or output
106 -rt <real> (0)
108 Integration limit for the -ot output (nm)
109 -ft <int> (0)
111 Number of frames in the -ot output, 0 is plot all
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114 gmx(1)
115 More information about GROMACS is available at <‐
117 http://www.gromacs.org/>.
118
120 2019, GROMACS development team
1212019.4 Oct 02, 2019 GMX-VANHOVE(1)