NAME

       g_density - calculates the density of the system

       VERSION 4.6.5

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 this number of slices.

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

       -ng int 1
        Number of groups of which to compute densities.

       -[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 2 Dec 2013                             g_density(1)