g_mydensity: Calculate local partial densities

g_mydensity is a modified version of the g_density GROMACS tool. It adds the possibility to calculate partial density landscape on a plane and partial density profile as a function of the distance to a group of atoms.

Only number and mass densities are supported yet.

Even if g_density regular features are available in g_mydensity you should use the original tool to use them.

Installation

g_mydensity depends on the GROMACS software package, which needs to be installed. Only versions 4.5.x have been tested, but g_mydensity might be compatible with other versions of GROMACS.

To install g_mydensity, GROMACS needs to be loaded. You can load it using:

source /path_to_gromacs/bin/GMXRC

Go into the source directory of the program, then run make. The g_mydensity executable should be created. Make sure that this executable is in the research path of your shell.

Usage

Here we assume that g_mydensity is in the research path of your shell. To get some help just run g_mydensity -h. All available options will be listed.

A classical use would be:

g_mydensity -f traj.xtc -s topol.tpr -n index.ndx -o order.xvg

GROMACS needs to be loaded for g_mydensity to work.

Basic arguments

So as most GROMACS tools, the basic arguments are:

• -f: the path to the trajectory to read;
• -s: the path to the topology (tpr file);
• -n: the path to an index file that describe the group of atoms you are interested in;

The -dens argument can be use to switch from mass density (when set to "mass", default) to number density (when set to "number"). The "charge" and "electron" options are not implemented.

Output control

The following arguments control the output. You can get either one or both of the possible outputs but you need to select at least one of them.

• -og: produce the partial density landscape; a file path can be given as argument. The produced file can be converted into a picture. See the Generate picture from landscapes_ section to know more about that.
• -od: produce the partial dentity profile as a function of distance to a group. Distance is calculated as a function of the center of mass of a reference group. The distance is calculated in 2D by default, the normal axis is ignored in the calculation. To calculate distances in 3D, use the -3d option.

Generate pictures from landscapes

The landscape output is a text file describing the order parameter values on a grid. The file format is not XPM like most grid outputs produced by GROMACS tools so the xpm2ps utility can not be used to produce usable pictures. The dispgrid python script aims to exploit the data and to produce pictures from them.

You need python 2.7, with the numpy and matplotlib modules to run dispgrid.

Basic usage of dispgrid is:

dispgrid input.dat output.png

See the help available by typing dispgrid -h for more features.