g_thickness: Calculate bilayer local thickness

Installation

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

To install g_thickness, 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_thickness executable should be created. Make sure that this executable is in the research path of your shell.

Usage

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

A classical use would be:

g_thickness -f traj.xtc -s topol.tpr -n index.ndx -og thickness_grid.dat

GROMACS needs to be loaded for g_thickness to work.

Required arguments

Three arguments are required for any use of the program. They 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 -d option defines the reference axis (i.e. the axis normal to the membrane). The axis is set at Z by default.

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 thickness landscape; a file path can be given as argument. The sampling for each cell of the grid is written in the file specified with the -osg option. The produced files can be converted into a picture. See the Generate picture from landscapes_ section to know more about that.
• -od: produce the thickness profile as a function of distance to a group. The sampling is written in the file given with the -osd option. Distance is calculated as a function of the center of mass of a reference group; the minimum distance can be used instead using the -nocom option.

Sampling control

There is two ways to adjust the sampling. The -sl option corresponds to the number of bins in the profile or to the number of cell per side in the landscape. The -sl2 option adjusts the number of cell per side on the second dimension of a profile; if it is not used then the value of -sl is used. See the following table to know which axis are controlled by -sl and -sl2.

====== ======= ========
``-d`` ``-sl`` ``-sl2``
====== ======= ========
x      y       z
y      x       z
z      x       y
====== ======= ========

The thickness averaging in a given cell or bin is done as follow: at each frame the atoms of interest in one leaflet in the considered volume are stored for this volume; the same is done for the other leaflet; every N frames, the center of mass of the stored atoms is calculated for each leaflet, then the distance between the two center of mass along the membrane normal axis is calculated and stored; at the end of the calculation, the distances are averaged. The number of frames N can be chosen using the -adt option. The bigger this value will be the bigger will be the sampling in each cell or bin, but the less accurate will be the result. If the value of -adt is negative or bigger than the number of frame in the trajectory, then distance between leaflets is calculated only once at the end.

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.