The algorithm of the GridMAT-MD program is discussed in greater detail in the corresponding publication. Here, we will give an overview of the main points of the calculations.|
The final data output for the thickness calculation is written as a raw data file, giving a single column list of thickness measurements. We have successfully interfaced the output of this program with XMatrix, a component of the Matpack software package, as well as Gnuplot. For data usage, please refer to the documentation provided with the program.
- Bilayer Thickness calculation:
- Based on a user-defined reference atom, each lipid in the top leaflet is assigned a paired lipid in the bottom leaflet, based on proximity in the x- and y- directions. The z-distance between these points is calculated. Periodicity is taken into account.
- The same step is repeated, only using the bottom leaflet as the reference, measuring the z-distance to the top leaflet.
- The distances with top and bottom leaflets as references are averaged, and the final output written to a generic ASCII .dat file.
- Area Per Lipid Headgroup calculation:
- The same calculations as in the thickness calculation are performed in order to assign thickness values to each grid point. A greater number of grid points is generally recommended to achieve good resolution.
- Protein atoms found within the lipid headgroups are assigned to grid points; this total area will be subtracted from the lateral area of the bilayer.
- The size of the system is determined from the dimensions of the unit cell.
- The recurrence of a thickness value for a given grid point determines the fraction of the total grid occupied by a single lipid. Based on this fraction, the area is calculated as that fraction of the total lateral area of the unit cell.
- The area for each individual lipid is written to a generic ASCII .dat file.
Area per lipid data is also printed to a generic .dat file, with the area of each lipid residue printed alongside the corresponding molecule. This format allows for simple, manual statistical analysis, or processing with standard *nix utilities like awk or Perl.