g_densmap(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_densmap(1)
NAME
g_densmap - calculates 2D planar or axial-radial density maps
VERSION 4.5.4-dev-20110404-bc5695c
SYNOPSIS
g_densmap -f traj.xtc -s topol.tpr -n index.ndx -od densmap.dat -o densmap.xpm -[no]h -[no]version -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
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. Optionally, 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.
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
-od densmap.dat Output, Opt.
Generic data file
-o densmap.xpm Output
X PixMap compatible matrix file
OTHER OPTIONS
-[no]hno
Print help info and quit
-[no]versionno
Print version 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
-[no]sumsno
Print density sums (1D map) to stdout
-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/>.
Mon 4 Apr 2011 g_densmap(1)