gmx density

Main Table of Contents VERSION 5.0-rc1-20140407-49a43a6-dirty

Synopsis

gmx density [-f [<.xtc/.trr/...>]] [-n [<.ndx>]] [-s [<.tpr/.tpb/...>]]
            [-ei [<.dat>]] [-o [<.xvg>]] [-nice ] [-b 

Description

gmx density computes partial densities across the box, using an index file.

For the total density of NPT simulations, use gmx energy instead.

Densities are in kg/m^3, and number densities or electron densities can also 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.

Options

Options to specify input and output files:

-f [<.xtc/.trr/...>] (traj.xtc) (Input)
Trajectory: xtc trr cpt trj gro g96 pdb tng
-n [<.ndx>] (index.ndx) (Input, Optional)
Index file
-s [<.tpr/.tpb/...>] (topol.tpr) (Input)
Run input file: tpr tpb tpa
-ei [<.dat>] (electrons.dat) (Input, Optional)
Generic data file
-o [<.xvg>] (density.xvg) (Output)
xvgr/xmgr file
Other options:

-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
-xvg <enum> (xmgrace)
xvg plot formatting: xmgrace, xmgr, none
-d <string> (Z)
Take the normal on the membrane in direction X, Y or Z.
-sl <int> (50)
Divide the box in this number of slices.
-dens <enum> (mass)
Density: mass, number, charge, electron
-ng <int> (1)
Number of groups of which to compute densities.
-[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.

Known Issues


http://www.gromacs.org