NAME
g_densmap - calculates 2D planar or axial-radial density maps
VERSION 4.0.1
SYNOPSIS
g_densmap -f traj.xtc -s topol.tpr -n index.ndx -o densmap.xpm -[no]h
-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 -unit
enum -dmin real -dmax real
DESCRIPTION
g_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.
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
normalization 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.
FILES
-f traj.xtc Input
Trajectory: xtc trr trj gro g96 pdb cpt
-s topol.tpr Input, Opt.
Structure+mass(db): tpr tpb tpa gro g96 pdb
-n index.ndx Input, Opt.
Index file
-o densmap.xpm Output
X PixMap compatible matrix file
OTHER OPTIONS
-[no]hno
Print help info and quit
-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]wno
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 or 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]mirrorno
Add the mirror image below the axial axis
-unit enum nm-3
Unit for the output: nm-3, nm-2 or count
-dmin real 0
Minimum density in output
-dmax real 0
Maximum density in output (0 means calculate it)
SEE ALSO
gromacs(7)
More information about GROMACS is available at
<http://www.gromacs.org/>.
Thu 16 Oct 2008 g_densmap(1)