1 .TH g_densmap 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
3 g_densmap - calculates 2D planar or axial-radial density maps
9 .BI "\-s" " topol.tpr "
10 .BI "\-n" " index.ndx "
11 .BI "\-od" " densmap.dat "
12 .BI "\-o" " densmap.xpm "
14 .BI "\-[no]version" ""
34 \&\fB g_densmap\fR computes 2D number\-density maps.
35 \&It can make planar and axial\-radial density maps.
36 \&The output \fB .xpm\fR file can be visualized with for instance xv
37 \&and can be converted to postscript with \fB xpm2ps\fR.
38 \&Optionally, output can be in text form to a \fB .dat\fR file with \fB \-od\fR, instead of the usual \fB .xpm\fR file with \fB \-o\fR.
42 \&The default analysis is a 2\-D number\-density map for a selected
43 \&group of atoms in the x\-y plane.
44 \&The averaging direction can be changed with the option \fB \-aver\fR.
45 \&When \fB \-xmin\fR and/or \fB \-xmax\fR are set only atoms that are
46 \&within the limit(s) in the averaging direction are taken into account.
47 \&The grid spacing is set with the option \fB \-bin\fR.
48 \&When \fB \-n1\fR or \fB \-n2\fR is non\-zero, the grid
49 \&size is set by this option.
50 \&Box size fluctuations are properly taken into account.
54 \&When options \fB \-amax\fR and \fB \-rmax\fR are set, an axial\-radial
55 \&number\-density map is made. Three groups should be supplied, the centers
56 \&of mass of the first two groups define the axis, the third defines the
57 \&analysis group. The axial direction goes from \-amax to +amax, where
58 \&the center is defined as the midpoint between the centers of mass and
59 \&the positive direction goes from the first to the second center of mass.
60 \&The radial direction goes from 0 to rmax or from \-rmax to +rmax
61 \&when the \fB \-mirror\fR option has been set.
65 \&The normalization of the output is set with the \fB \-unit\fR option.
66 \&The default produces a true number density. Unit \fB nm\-2\fR leaves out
67 \&the normalization for the averaging or the angular direction.
68 \&Option \fB count\fR produces the count for each grid cell.
69 \&When you do not want the scale in the output to go
70 \&from zero to the maximum density, you can set the maximum
71 \&with the option \fB \-dmax\fR.
75 Trajectory: xtc trr trj gro g96 pdb cpt
77 .BI "\-s" " topol.tpr"
79 Structure+mass(db): tpr tpb tpa gro g96 pdb
81 .BI "\-n" " index.ndx"
85 .BI "\-od" " densmap.dat"
89 .BI "\-o" " densmap.xpm"
91 X PixMap compatible matrix file
95 Print help info and quit
97 .BI "\-[no]version" "no "
98 Print version info and quit
100 .BI "\-nice" " int" " 19"
103 .BI "\-b" " time" " 0 "
104 First frame (ps) to read from trajectory
106 .BI "\-e" " time" " 0 "
107 Last frame (ps) to read from trajectory
109 .BI "\-dt" " time" " 0 "
110 Only use frame when t MOD dt = first time (ps)
113 View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files
115 .BI "\-bin" " real" " 0.02 "
118 .BI "\-aver" " enum" " z"
119 The direction to average over: \fB z\fR, \fB y\fR or \fB x\fR
121 .BI "\-xmin" " real" " \-1 "
122 Minimum coordinate for averaging
124 .BI "\-xmax" " real" " \-1 "
125 Maximum coordinate for averaging
127 .BI "\-n1" " int" " 0"
128 Number of grid cells in the first direction
130 .BI "\-n2" " int" " 0"
131 Number of grid cells in the second direction
133 .BI "\-amax" " real" " 0 "
134 Maximum axial distance from the center
136 .BI "\-rmax" " real" " 0 "
137 Maximum radial distance
139 .BI "\-[no]mirror" "no "
140 Add the mirror image below the axial axis
142 .BI "\-[no]sums" "no "
143 Print density sums (1D map) to stdout
145 .BI "\-unit" " enum" " nm\-3"
146 Unit for the output: \fB nm\-3\fR, \fB nm\-2\fR or \fB count\fR
148 .BI "\-dmin" " real" " 0 "
149 Minimum density in output
151 .BI "\-dmax" " real" " 0 "
152 Maximum density in output (0 means calculate it)
157 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.