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)