Main Table of Contents

Thu 26 Aug 2010


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:
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.


-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]h gmx_bool no Print help info and quit
-[no]version gmx_bool no 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]w gmx_bool no 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 #nr slices.
-dens enum mass Density: mass, number, charge or electron
-ng int 1 Number of groups to compute densities of
-[no]symm gmx_bool no Symmetrize the density along the axis, with respect to the center. Useful for bilayers.
-[no]center gmx_bool 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.

Known problems