g_density_d (1) Linux Manual Page

g_density – calculates the density of the system

VERSION 4.0.1

Synopsis

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

Description

Compute partial densities across the box, using an index file. Densities in kg/m3, number densities or electron densities can 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

-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

-[no]xvgryes
 Add specific codes (legends etc.) in the output xvg files for the xmgrace program

-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/>.