1 .TH g_vanhove 1 "Fri 19 Apr 2013" "" "GROMACS suite, VERSION 4.5.7"
3 g_vanhove - calculates Van Hove displacement functions
9 .BI "\-s" " topol.tpr "
10 .BI "\-n" " index.ndx "
11 .BI "\-om" " vanhove.xpm "
12 .BI "\-or" " vanhove_r.xvg "
13 .BI "\-ot" " vanhove_t.xvg "
15 .BI "\-[no]version" ""
27 .BI "\-nlevels" " int "
33 \&\fB g_vanhove\fR computes the Van Hove correlation function.
34 \&The Van Hove G(r,t) is the probability that a particle that is at r_0
35 \&at time zero can be found at position r_0+r at time t.
36 \&\fB g_vanhove\fR determines G not for a vector r, but for the length of r.
37 \&Thus it gives the probability that a particle moves a distance of r
39 \&Jumps across the periodic boundaries are removed.
40 \&Corrections are made for scaling due to isotropic
41 \&or anisotropic pressure coupling.
45 \&With option \fB \-om\fR the whole matrix can be written as a function
46 \&of t and r or as a function of sqrt(t) and r (option \fB \-sqrt\fR).
50 \&With option \fB \-or\fR the Van Hove function is plotted for one
51 \&or more values of t. Option \fB \-nr\fR sets the number of times,
52 \&option \fB \-fr\fR the number spacing between the times.
53 \&The binwidth is set with option \fB \-rbin\fR. The number of bins
54 \&is determined automatically.
58 \&With option \fB \-ot\fR the integral up to a certain distance
59 \&(option \fB \-rt\fR) is plotted as a function of time.
63 \&For all frames that are read the coordinates of the selected particles
64 \&are stored in memory. Therefore the program may use a lot of memory.
65 \&For options \fB \-om\fR and \fB \-ot\fR the program may be slow.
66 \&This is because the calculation scales as the number of frames times
67 \&\fB \-fm\fR or \fB \-ft\fR.
68 \&Note that with the \fB \-dt\fR option the memory usage and calculation
69 \&time can be reduced.
73 Trajectory: xtc trr trj gro g96 pdb cpt
75 .BI "\-s" " topol.tpr"
77 Structure+mass(db): tpr tpb tpa gro g96 pdb
79 .BI "\-n" " index.ndx"
83 .BI "\-om" " vanhove.xpm"
85 X PixMap compatible matrix file
87 .BI "\-or" " vanhove_r.xvg"
91 .BI "\-ot" " vanhove_t.xvg"
97 Print help info and quit
99 .BI "\-[no]version" "no "
100 Print version info and quit
102 .BI "\-nice" " int" " 19"
105 .BI "\-b" " time" " 0 "
106 First frame (ps) to read from trajectory
108 .BI "\-e" " time" " 0 "
109 Last frame (ps) to read from trajectory
111 .BI "\-dt" " time" " 0 "
112 Only use frame when t MOD dt = first time (ps)
115 View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files
117 .BI "\-xvg" " enum" " xmgrace"
118 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR
120 .BI "\-sqrt" " real" " 0 "
121 Use sqrt(t) on the matrix axis which binspacing in sqrt(ps)
123 .BI "\-fm" " int" " 0"
124 Number of frames in the matrix, 0 is plot all
126 .BI "\-rmax" " real" " 2 "
127 Maximum r in the matrix (nm)
129 .BI "\-rbin" " real" " 0.01 "
130 Binwidth in the matrix and for \fB \-or\fR (nm)
132 .BI "\-mmax" " real" " 0 "
133 Maximum density in the matrix, 0 is calculate (1/nm)
135 .BI "\-nlevels" " int" " 81"
136 Number of levels in the matrix
138 .BI "\-nr" " int" " 1"
139 Number of curves for the \fB \-or\fR output
141 .BI "\-fr" " int" " 0"
142 Frame spacing for the \fB \-or\fR output
144 .BI "\-rt" " real" " 0 "
145 Integration limit for the \fB \-ot\fR output (nm)
147 .BI "\-ft" " int" " 0"
148 Number of frames in the \fB \-ot\fR output, 0 is plot all
153 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.