1GMX-DENSMAP(1)                      GROMACS                     GMX-DENSMAP(1)
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NAME

6       gmx-densmap - Calculate 2D planar or axial-radial density maps
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SYNOPSIS

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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DESCRIPTION

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.
20       Optionally, output can be in text form to a .dat file with -od, instead
21       of the usual .xpm file with -o.
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23       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.
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31       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.
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40       The normalization of the output is set  with  the  -unit  option.   The
41       default  produces  a true number density. Unit nm-2 leaves out the nor‐
42       malization for the averaging or the angular  direction.   Option  count
43       produces  the count for each grid cell.  When you do not want the scale
44       in the output to go from zero to the maximum density, you can  set  the
45       maximum with the option -dmax.
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OPTIONS

48       Options to specify input files:
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50       -f [<.xtc/.trr/…>] (traj.xtc)
51              Trajectory: xtc trr cpt gro g96 pdb tng
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53       -s [<.tpr/.gro/…>] (topol.tpr) (Optional)
54              Structure+mass(db): tpr gro g96 pdb brk ent
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56       -n [<.ndx>] (index.ndx) (Optional)
57              Index file
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59       Options to specify output files:
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61       -od [<.dat>] (densmap.dat) (Optional)
62              Generic data file
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64       -o [<.xpm>] (densmap.xpm)
65              X PixMap compatible matrix file
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67       Other options:
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69       -b <time> (0)
70              Time of first frame to read from trajectory (default unit ps)
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72       -e <time> (0)
73              Time of last frame to read from trajectory (default unit ps)
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75       -dt <time> (0)
76              Only use frame when t MOD dt = first time (default unit ps)
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78       -[no]w (no)
79              View output .xvg, .xpm, .eps and .pdb files
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81       -bin <real> (0.02)
82              Grid size (nm)
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84       -aver <enum> (z)
85              The direction to average over: z, y, x
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87       -xmin <real> (-1)
88              Minimum coordinate for averaging
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90       -xmax <real> (-1)
91              Maximum coordinate for averaging
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93       -n1 <int> (0)
94              Number of grid cells in the first direction
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96       -n2 <int> (0)
97              Number of grid cells in the second direction
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99       -amax <real> (0)
100              Maximum axial distance from the center
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102       -rmax <real> (0)
103              Maximum radial distance
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105       -[no]mirror (no)
106              Add the mirror image below the axial axis
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108       -[no]sums (no)
109              Print density sums (1D map) to stdout
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111       -unit <enum> (nm-3)
112              Unit for the output: nm-3, nm-2, count
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114       -dmin <real> (0)
115              Minimum density in output
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117       -dmax <real> (0)
118              Maximum density in output (0 means calculate it)
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SEE ALSO

121       gmx(1)
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123       More     information    about    GROMACS    is    available    at    <‐
124       http://www.gromacs.org/>.
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127       2019, GROMACS development team
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1322019.4                           Oct 02, 2019                   GMX-DENSMAP(1)
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