g_density(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c				      g_density(1)

NAME

       g_density - calculates the density of the system

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       g_density  -f  traj.xtc	-n  index.ndx -s topol.tpr -ei electrons.dat -o density.xvg -[no]h -[no]version -nice int -b time -e time -dt time
       -[no]w -xvg enum -d string -sl int -dens enum -ng int -[no]symm -[no]center

DESCRIPTION

       Compute partial densities across the box, using an index file.

       For the total density of NPT simulations, use  g_energy instead.

       Densities are in kg/m3, and number densities or electron densities can also be calculated. For electron densities, a  file  describing  the
       number of electrons for each type of atom should be provided using  -ei.  It should look like:

	   2

	   atomname = nrelectrons

	   atomname = nrelectrons

       The first line contains the number of lines to read from the file.  There should be one line for each unique atom name in your system.  The
       number of electrons for each atom is modified by its atomic partial charge.

FILES

       -f traj.xtc Input
	Trajectory: xtc trr trj gro g96 pdb cpt

       -n index.ndx Input, Opt.
	Index file

       -s topol.tpr Input
	Run input file: tpr tpb tpa

       -ei electrons.dat Input, Opt.
	Generic data file

       -o density.xvg Output
	xvgr/xmgr 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

       -xvg enum xmgrace
	xvg plot formatting:  xmgrace,	xmgr or  none

       -d string Z
	Take the normal on the membrane in direction X, Y or Z.

       -sl int 50
	Divide the box in nr slices.

       -dens enum mass
	Density:  mass,  number,  charge or  electron

       -ng int 1
	Number of groups to compute densities of

       -[no]symmno
	Symmetrize the density along the axis, with respect to the center. Useful for bilayers.

       -[no]centerno
	Shift the center of mass along the axis to zero. This means if your axis is Z and your box is bX, bY, bZ, the center of mass  will  be	at
       bX/2, bY/2, 0.

KNOWN PROBLEMS

       - When calculating electron densities, atomnames are used instead of types. This is bad.

SEE ALSO

       gromacs(7)

       More information about GROMACS is available at <http://www.gromacs.org/>.

								  Mon 4 Apr 2011						      g_density(1)