g_density

VERSION 3.1
Thu 28 Feb 2002

Description

Compute partial densities across the box, using an index file. Densities in kg/m^3, 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

option	filename	type	description
`-f`	`traj.xtc`	Input	Generic trajectory: xtc trr trj gro g96 pdb
`-n`	`index.ndx`	Input, Opt.	Index file
`-s`	`topol.tpr`	Input	Generic run input: tpr tpb tpa
`-ei`	`electrons.dat`	Input, Opt.	Generic data file
`-o`	`density.xvg`	Output	xvgr/xmgr file

Other options

option	type	default	description
`-[no]h`	bool	`no`	Print help info and quit
`-[no]X`	bool	`no`	Use dialog box GUI to edit command line options
`-nice`	int	`19`	Set the nicelevel
`-b`	time	`-1`	First frame (ps) to read from trajectory
`-e`	time	`-1`	Last frame (ps) to read from trajectory
`-dt`	time	`-1`	Only use frame when t MOD dt = first time (ps)
`-[no]w`	bool	`no`	View output xvg, xpm, eps and pdb files
`-d`	string	`Z`	Take the normal on the membrane in direction X, Y or Z.
`-sl`	int	`10`	Divide the box in #nr slices.
`-[no]number`	bool	`no`	Calculate number density instead of mass density. Hydrogens are not counted!
`-[no]ed`	bool	`no`	Calculate electron density instead of mass density
`-[no]count`	bool	`no`	Only count atoms in slices, no densities. Hydrogens are not counted

When calculating electron densities, atomnames are used instead of types. This is bad.
When calculating number densities, atoms with names that start with H are not counted. This may be surprising if you use hydrogens with names like OP3.

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