1GMX-DENSMAP(1) GROMACS GMX-DENSMAP(1)
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6 gmx-densmap - Calculate 2D planar or axial-radial density maps
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9 gmx densmap [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
10 [-od [<.dat>]] [-o [<.xpm>]] [-b <time>] [-e <time>]
11 [-dt <time>] [-[no]w] [-bin <real>] [-aver <enum>]
12 [-xmin <real>] [-xmax <real>] [-n1 <int>] [-n2 <int>]
13 [-amax <real>] [-rmax <real>] [-[no]mirror] [-[no]sums]
14 [-unit <enum>] [-dmin <real>] [-dmax <real>]
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17 gmx densmap computes 2D number-density maps. It can make planar and
18 axial-radial density maps. The output .xpm file can be visualized with
19 for instance xv and can be converted to postscript with xpm2ps. Op‐
20 tionally, output can be in text form to a .dat file with -od, instead
21 of the usual .xpm file with -o.
22 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 are
26 within the limit(s) in the averaging direction are taken into account.
27 The grid spacing is set with the option -bin. When -n1 or -n2 is
28 non-zero, the grid size is set by this option. Box size fluctuations
29 are properly taken into account.
30 When options -amax and -rmax are set, an axial-radial number-density
32 map is made. Three groups should be supplied, the centers of mass of
33 the first two groups define the axis, the third defines the analysis
34 group. The axial direction goes from -amax to +amax, where the center
35 is defined as the midpoint between the centers of mass and the positive
36 direction goes from the first to the second center of mass. The radial
37 direction goes from 0 to rmax or from -rmax to +rmax when the -mirror
38 option has been set.
39 The normalization of the output is set with the -unit option. The de‐
41 fault produces a true number density. Unit nm-2 leaves out the normal‐
42 ization for the averaging or the angular direction. Option count pro‐
43 duces the count for each grid cell. When you do not want the scale in
44 the output to go from zero to the maximum density, you can set the max‐
45 imum with the option -dmax.
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48 Options to specify input files:
49 -f [<.xtc/.trr/...>] (traj.xtc)
51 Trajectory: xtc trr cpt gro g96 pdb tng
52 -s [<.tpr/.gro/...>] (topol.tpr) (Optional)
54 Structure+mass(db): tpr gro g96 pdb brk ent
55 -n [<.ndx>] (index.ndx) (Optional)
57 Index file
58 Options to specify output files:
60 -od [<.dat>] (densmap.dat) (Optional)
62 Generic data file
63 -o [<.xpm>] (densmap.xpm)
65 X PixMap compatible matrix file
66 Other options:
68 -b <time> (0)
70 Time of first frame to read from trajectory (default unit ps)
71 -e <time> (0)
73 Time of last frame to read from trajectory (default unit ps)
74 -dt <time> (0)
76 Only use frame when t MOD dt = first time (default unit ps)
77 -[no]w (no)
79 View output .xvg, .xpm, .eps and .pdb files
80 -bin <real> (0.02)
82 Grid size (nm)
83 -aver <enum> (z)
85 The direction to average over: z, y, x
86 -xmin <real> (-1)
88 Minimum coordinate for averaging
89 -xmax <real> (-1)
91 Maximum coordinate for averaging
92 -n1 <int> (0)
94 Number of grid cells in the first direction
95 -n2 <int> (0)
97 Number of grid cells in the second direction
98 -amax <real> (0)
100 Maximum axial distance from the center
101 -rmax <real> (0)
103 Maximum radial distance
104 -[no]mirror (no)
106 Add the mirror image below the axial axis
107 -[no]sums (no)
109 Print density sums (1D map) to stdout
110 -unit <enum> (nm-3)
112 Unit for the output: nm-3, nm-2, count
113 -dmin <real> (0)
115 Minimum density in output
116 -dmax <real> (0)
118 Maximum density in output (0 means calculate it)
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121 gmx(1)
122 More information about GROMACS is available at <‐
124 http://www.gromacs.org/>.
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127 2022, GROMACS development team
1282022.3 Sep 02, 2022 GMX-DENSMAP(1)