1g_densmap(1) GROMACS suite, VERSION 4.5 g_densmap(1)
2
6 g_densmap - calculates 2D planar or axial-radial density maps
7 VERSION 4.5
9
11 g_densmap -f traj.xtc -s topol.tpr -n index.ndx -od densmap.dat -o
12 densmap.xpm -[no]h -[no]version -nice int -b time -e time -dt time
13 -[no]w -bin real -aver enum -xmin real -xmax real -n1 int -n2 int -amax
14 real -rmax real -[no]mirror -[no]sums -unit enum -dmin real -dmax real
15
17 g_densmap computes 2D number-density maps. It can make planar and
18 axial-radial density maps. The output .xpm file can be visualized
19 with for instance xv and can be converted to postscript with xpm2ps.
20 Optionally, output can be in text form to a .dat file.
21 The default analysis is a 2-D number-density map for a selected group
24 of atoms in the x-y plane. The averaging direction can be changed with
25 the option -aver. When -xmin and/or -xmax are set only atoms that
26 are within the limit(s) in the averaging direction are taken into
27 account. The grid spacing is set with the option -bin. When -n1 or
28 -n2 is non-zero, the grid size is set by this option. Box size fluctu‐
29 ations are properly taken into account.
30 When options -amax and -rmax are set, an axial-radial number-density
33 map is made. Three groups should be supplied, the centers of mass of
34 the first two groups define the axis, the third defines the analysis
35 group. The axial direction goes from -amax to +amax, where the center
36 is defined as the midpoint between the centers of mass and the positive
37 direction goes from the first to the second center of mass. The radial
38 direction goes from 0 to rmax or from -rmax to +rmax when the -mirror
39 option has been set.
40 The normalization of the output is set with the -unit option. The
43 default produces a true number density. Unit nm-2 leaves out the nor‐
44 malization for the averaging or the angular direction. Option count
45 produces the count for each grid cell. When you do not want the scale
46 in the output to go from zero to the maximum density, you can set the
47 maximum with the option -dmax.
48
50 -f traj.xtc Input
51 Trajectory: xtc trr trj gro g96 pdb cpt
52 -s topol.tpr Input, Opt.
54 Structure+mass(db): tpr tpb tpa gro g96 pdb
55 -n index.ndx Input, Opt.
57 Index file
58 -od densmap.dat Output, Opt.
60 Generic data file
61 -o densmap.xpm Output
63 X PixMap compatible matrix file
64
67 -[no]hno
68 Print help info and quit
69 -[no]versionno
71 Print version info and quit
72 -nice int 19
74 Set the nicelevel
75 -b time 0
77 First frame (ps) to read from trajectory
78 -e time 0
80 Last frame (ps) to read from trajectory
81 -dt time 0
83 Only use frame when t MOD dt = first time (ps)
84 -[no]wno
86 View output xvg, xpm, eps and pdb files
87 -bin real 0.02
89 Grid size (nm)
90 -aver enum z
92 The direction to average over: z, y or x
93 -xmin real -1
95 Minimum coordinate for averaging
96 -xmax real -1
98 Maximum coordinate for averaging
99 -n1 int 0
101 Number of grid cells in the first direction
102 -n2 int 0
104 Number of grid cells in the second direction
105 -amax real 0
107 Maximum axial distance from the center
108 -rmax real 0
110 Maximum radial distance
111 -[no]mirrorno
113 Add the mirror image below the axial axis
114 -[no]sumsno
116 Print density sums (1D map) to stdout
117 -unit enum nm-3
119 Unit for the output: nm-3, nm-2 or count
120 -dmin real 0
122 Minimum density in output
123 -dmax real 0
125 Maximum density in output (0 means calculate it)
126
129 gromacs(7)
130 More information about GROMACS is available at <http://www.gro‐
132 macs.org/>.
133 Thu 26 Aug 2010 g_densmap(1)