gmx densmap [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]] [-od [<.dat>]] [-o [<.xpm>]] [-b <time>] [-e <time>] [-dt <time>] [-[no]w] [-bin <real>] [-aver <enum>] [-xmin <real>] [-xmax <real>] [-n1 <int>] [-n2 <int>] [-amax <real>] [-rmax <real>] [-[no]mirror] [-[no]sums] [-unit <enum>] [-dmin <real>] [-dmax <real>]
gmx densmap computes 2D number-density maps.
It can make planar and axial-radial density maps.
The output .xpm file can be visualized with for instance xv
and can be converted to postscript with
Optionally, output can be in text form to a .dat file with
instead of the usual .xpm file with
The default analysis is a 2-D number-density map for a selected
group of atoms in the x-y plane.
The averaging direction can be changed with the option
-xmax are set only atoms that are
within the limit(s) in the averaging direction are taken into account.
The grid spacing is set with the option
-n2 is non-zero, the grid
size is set by this option.
Box size fluctuations are properly taken into account.
-rmax are set, an axial-radial
number-density map is made. Three groups should be supplied, the centers
of mass of the first two groups define the axis, the third defines the
analysis group. The axial direction goes from -amax to +amax, where
the center is defined as the midpoint between the centers of mass and
the positive direction goes from the first to the second center of mass.
The radial direction goes from 0 to rmax or from -rmax to +rmax
-mirror option has been set.
The normalization of the output is set with the
The default produces a true number density. Unit
nm-2 leaves out
the normalization for the averaging or the angular direction.
count produces the count for each grid cell.
When you do not want the scale in the output to go
from zero to the maximum density, you can set the maximum
with the option
Options to specify input files:
-s[<.tpr/.gro/…>] (topol.tpr) (Optional)
-n[<.ndx>] (index.ndx) (Optional)
Options to specify output files:
-od[<.dat>] (densmap.dat) (Optional)
Generic data file
X PixMap compatible matrix file
Time of first frame to read from trajectory (default unit ps)
Time of last frame to read from trajectory (default unit ps)
Only use frame when t MOD dt = first time (default unit ps)
Grid size (nm)
The direction to average over: z, y, x
Minimum coordinate for averaging
Maximum coordinate for averaging
Number of grid cells in the first direction
Number of grid cells in the second direction
Maximum axial distance from the center
Maximum radial distance
Add the mirror image below the axial axis
Print density sums (1D map) to stdout
Unit for the output: nm-3, nm-2, count
Minimum density in output
Maximum density in output (0 means calculate it)