I plot thickness.dat files with xmatrix and gnuplot but I cannot plot area per lipid.dat files neither with Xmatrix nor with Gnuplot. Does anyone know the corresponding command line for Gnuplot or the the tutorial for plotting area per lipid.dat.
I think Xmatrix can just read column output file formats . My area per lipid file is a simple file with three column data, same as what has been shown in GridMAT-MD manual v2.0.
The information bellow figure 6 in GridMAT-MD v2.0 says that the figure has been shown with Xmatrix, but how?
In a general answer:
"the area per lipid data can be 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".
An answer including the details is as follows:
(1) For the Bilayer Thickness calculation please note to the following steps
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.
(2) The z-distance between these points is calculated. Periodicity can be taken into account.
(3) The same step can be repeated, only using the bottom leaflet as the reference, measuring the z-distance to the top leaflet.
(4) The distances with top and bottom leaflets as references are averaged, and the final output written to a generic ASCII .dat file.
So after the above calculating for the "Area Per Lipid Headgroup calculation" please note to the following steps:
(1) The same calculations as in the thickness calculation might be performed in order to assign thickness values to each grid point. A greater number of grid points is generally recommended to achieve good resolution.
(2) 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.
(3) The size of the system is determined from the dimensions of the unit cell.
(4)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 can be calculated as that fraction of the total lateral area of the unit cell.
(5)The area for each individual lipid can be written to a generic ASCII .dat file.
(6) The final data output for the thickness calculation can be written as a raw data file, giving a single column list of thickness measurements.
(7) The interfaced of the output of this program with XMatrix, a component of the Matpack software package, as well as Gnuplot.
(8) For data usage, please refer to the documentation provided with the program.
(9) Area per lipid data is also can be printed to a generic .dat file, with the area of each lipid residue printed alongside the corresponding molecule.
(10)This format allows for simple, manual statistical analysis, or processing with standard *nix utilities like awk or Perl.
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