1GMX-VANHOVE(1)                      GROMACS                     GMX-VANHOVE(1)
2
3
4

NAME

6       gmx-vanhove - Compute Van Hove displacement and correlation functions
7

SYNOPSIS

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>]
15

DESCRIPTION

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
25       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
28       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
33       With  option  -ot the integral up to a certain distance (option -rt) is
34       plotted as a function of time.
35
36       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.
42

OPTIONS

44       Options to specify input files:
45
46       -f [<.xtc/.trr/…>] (traj.xtc)
47              Trajectory: xtc trr cpt gro g96 pdb tng
48
49       -s [<.tpr/.gro/…>] (topol.tpr)
50              Structure+mass(db): tpr gro g96 pdb brk ent
51
52       -n [<.ndx>] (index.ndx) (Optional)
53              Index file
54
55       Options to specify output files:
56
57       -om [<.xpm>] (vanhove.xpm) (Optional)
58              X PixMap compatible matrix file
59
60       -or [<.xvg>] (vanhove_r.xvg) (Optional)
61              xvgr/xmgr file
62
63       -ot [<.xvg>] (vanhove_t.xvg) (Optional)
64              xvgr/xmgr file
65
66       Other options:
67
68       -b <time> (0)
69              Time of first frame to read from trajectory (default unit ps)
70
71       -e <time> (0)
72              Time of last frame to read from trajectory (default unit ps)
73
74       -dt <time> (0)
75              Only use frame when t MOD dt = first time (default unit ps)
76
77       -[no]w (no)
78              View output .xvg, .xpm, .eps and .pdb files
79
80       -xvg <enum> (xmgrace)
81              xvg plot formatting: xmgrace, xmgr, none
82
83       -sqrt <real> (0)
84              Use sqrt(t) on the matrix axis which binspacing # in sqrt(ps)
85
86       -fm <int> (0)
87              Number of frames in the matrix, 0 is plot all
88
89       -rmax <real> (2)
90              Maximum r in the matrix (nm)
91
92       -rbin <real> (0.01)
93              Binwidth in the matrix and for -or (nm)
94
95       -mmax <real> (0)
96              Maximum density in the matrix, 0 is calculate (1/nm)
97
98       -nlevels <int> (81)
99              Number of levels in the matrix
100
101       -nr <int> (1)
102              Number of curves for the -or output
103
104       -fr <int> (0)
105              Frame spacing for the -or output
106
107       -rt <real> (0)
108              Integration limit for the -ot output (nm)
109
110       -ft <int> (0)
111              Number of frames in the -ot output, 0 is plot all
112

SEE ALSO

114       gmx(1)
115
116       More     information    about    GROMACS    is    available    at    <‐
117       http://www.gromacs.org/>.
118
120       2019, GROMACS development team
121
122
123
124
1252018.7                           May 29, 2019                   GMX-VANHOVE(1)
Impressum