table of contents
g_density(1) | GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c | g_density(1) |
NAME¶
g_density - calculates the density of the systemSYNOPSIS¶
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]centerDESCRIPTION¶
Compute partial densities across the box, using an index file.FILES¶
-f traj.xtc InputTrajectory: xtc trr trj gro g96 pdb cpt
Index file
Run input file: tpr tpb tpa
Generic data file
xvgr/xmgr file
OTHER OPTIONS¶
-[no]hnoPrint help info and quit
Print version info and quit
Set the nicelevel
First frame (ps) to read from trajectory
Last frame (ps) to read from trajectory
Only use frame when t MOD dt = first time (ps)
View output .xvg, .xpm, .eps and .pdb files
xvg plot formatting: xmgrace, xmgr or none
Take the normal on the membrane in direction X, Y or Z.
Divide the box in nr slices.
Density: mass, number, charge or electron
Number of groups to compute densities of
Symmetrize the density along the axis, with respect to the center. Useful for bilayers.
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)Mon 4 Apr 2011 |