g_vanhove(1)

1g_vanhove(1)              GROMACS suite, VERSION 4.5              g_vanhove(1)
2
3
4

NAME

6       g_vanhove - calculates Van Hove displacement functions
7
8       VERSION 4.5
9

SYNOPSIS

11       g_vanhove  -f  traj.xtc  -s  topol.tpr -n index.ndx -om vanhove.xpm -or
12       vanhove_r.xvg -ot vanhove_t.xvg -[no]h -[no]version -nice int  -b  time
13       -e  time  -dt time -[no]w -xvg enum -sqrt real -fm int -rmax real -rbin
14       real -mmax real -nlevels int -nr int -fr int -rt real -ft int
15

DESCRIPTION

17       g_vanhove computes the Van Hove correlation  function.   The  Van  Hove
18       G(r,t)  is  the  probability that a particle that is at r0 at time zero
19       can be found at position r0+r at time t.  g_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
26       With option  -om the whole matrix can be written as a function of t and
27       r or as a function of sqrt(t) and r (option  -sqrt).
28
29
30       With  option  -or the Van Hove function is plotted for one or more val‐
31       ues of t. Option  -nr sets the number of times, option  -fr the  number
32       spacing between the times.  The binwidth is set with option  -rbin. The
33       number of bins is determined automatically.
34
35
36       With option  -ot the integral up to a certain distance (option  -rt) is
37       plotted as a function of time.
38
39
40       For  all frames that are read the coordinates of the selected particles
41       are stored in memory. Therefore the program may use a  lot  of  memory.
42       For options  -om and  -ot the program may be slow.  This is because the
43       calculation scales as the number of frames times  -fm  or   -ft.   Note
44       that  with the  -dt option the memory usage and calculation time can be
45       reduced.
46

FILES

48       -f traj.xtc Input
49        Trajectory: xtc trr trj gro g96 pdb cpt
50
51       -s topol.tpr Input
52        Structure+mass(db): tpr tpb tpa gro g96 pdb
53
54       -n index.ndx Input, Opt.
55        Index file
56
57       -om vanhove.xpm Output, Opt.
58        X PixMap compatible matrix file
59
60       -or vanhove_r.xvg Output, Opt.
61        xvgr/xmgr file
62
63       -ot vanhove_t.xvg Output, Opt.
64        xvgr/xmgr file
65
66

OTHER OPTIONS

68       -[no]hno
69        Print help info and quit
70
71       -[no]versionno
72        Print version info and quit
73
74       -nice int 19
75        Set the nicelevel
76
77       -b time 0
78        First frame (ps) to read from trajectory
79
80       -e time 0
81        Last frame (ps) to read from trajectory
82
83       -dt time 0
84        Only use frame when t MOD dt = first time (ps)
85
86       -[no]wno
87        View output xvg, xpm, eps and pdb files
88
89       -xvg enum xmgrace
90        xvg plot formatting:  xmgrace,  xmgr or  none
91
92       -sqrt real 0
93        Use sqrt(t) on the matrix axis which binspacing  in sqrt(ps)
94
95       -fm int 0
96        Number of frames in the matrix, 0 is plot all
97
98       -rmax real 2
99        Maximum r in the matrix (nm)
100
101       -rbin real 0.01
102        Binwidth in the matrix and for -or (nm)
103
104       -mmax real 0
105        Maximum density in the matrix, 0 is calculate (1/nm)
106
107       -nlevels int 81
108        Number of levels in the matrix
109
110       -nr int 1
111        Number of curves for the -or output
112
113       -fr int 0
114        Frame spacing for the -or output
115
116       -rt real 0
117        Integration limit for the -ot output (nm)
118
119       -ft int 0
120        Number of frames in the -ot output, 0 is plot all
121
122

NAME

SYNOPSIS

DESCRIPTION

FILES

OTHER OPTIONS

SEE ALSO