man g_density (Commandes) - g_density VERSION 3.3_beta_20050823
NAME
g_density VERSION 3.3_beta_20050823
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 -[no]number -[no]ed -[no]count -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 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 xml
-ei electrons.dat Input, Opt. Generic data file
-o density.xvg Output xvgr/xmgr file
OTHER OPTIONS
-[no]h no 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]w no View output xvg, xpm, eps and pdb files
-[no]xvgr yes 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 10 Divide the box in nr slices.
-[no]number no Calculate number density instead of mass density. Hydrogens are not counted!
-[no]ed no Calculate electron density instead of mass density
-[no]count no Only count atoms in slices, no densities. Hydrogens are not counted
-ng int 0 Number of groups to compute densities of
-[no]symm no Symmetrize the density along the axis, with respect to the center. Useful for bilayers.
-[no]center no 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.
- 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.