debian man page for g_densmap

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)