gmx-densmap(1) GROMACS Manual gmx-densmap(1)NAMEgmx-densmap - Calculate 2D planar or axial-radial density maps
SYNOPSIS
gmx densmap [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]]
[-n [<.ndx>]] [-od [<.dat>]] [-o [<.xpm>]] [-nice <int>]
[-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>]
DESCRIPTION
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 xpm2ps. Option‐
ally, output can be in text form to a .dat file with -od, instead of
the usual .xpm file with -o.
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 -aver. When -xmin and/or -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 -bin. When -n1 or -n2 is
non-zero, the grid size is set by this option. Box size fluctuations
are properly taken into account.
When options -amax and -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 when the -mirror
option has been set.
The normalization of the output is set with the -unit option. The
default produces a true number density. Unit nm-2 leaves out the nor‐
malization for the averaging or the angular direction. Option 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 -dmax.
OPTIONS
Options to specify input and output files:
-f [<.xtc/.trr/...>] (traj.xtc) (Input)
Trajectory: xtc trr cpt trj gro g96 pdb tng
-s [<.tpr/.tpb/...>] (topol.tpr) (Input, Optional)
Structure+mass(db): tpr tpb tpa gro g96 pdb brk ent
-n [<.ndx>] (index.ndx) (Input, Optional)
Index file
-od [<.dat>] (densmap.dat) (Output, Optional)
Generic data file
-o [<.xpm>] (densmap.xpm) (Output)
X PixMap compatible matrix file
Other options:
-nice <int> (19)
Set the nicelevel
-b <time> (0)
First frame (ps) to read from trajectory
-e <time> (0)
Last frame (ps) to read from trajectory
-dt <time> (0)
Only use frame when t MOD dt = first time (ps)
-[no]w (no)
View output .xvg, .xpm, .eps and .pdb files
-bin <real> (0.02)
Grid size (nm)
-aver <enum> (z)
The direction to average over: z, y, x
-xmin <real> (-1)
Minimum coordinate for averaging
-xmax <real> (-1)
Maximum coordinate for averaging
-n1 <int> (0)
Number of grid cells in the first direction
-n2 <int> (0)
Number of grid cells in the second direction
-amax <real> (0)
Maximum axial distance from the center
-rmax <real> (0)
Maximum radial distance
-[no]mirror (no)
Add the mirror image below the axial axis
-[no]sums (no)
Print density sums (1D map) to stdout
-unit <enum> (nm-3)
Unit for the output: nm-3, nm-2, count
-dmin <real> (0)
Minimum density in output
-dmax <real> (0)
Maximum density in output (0 means calculate it)
SEE ALSOgromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6gmx-densmap(1)
