AreaPerLipid

Area per lipid tool

The Area per Lipid tool calculates both the total area per lipid and the area per lipid of each lipid species of the membrane under analysis. To this end, it uses a user-customizable selection of one key atom (i.e. sterols) or a triad of atoms (i.e. phospho- or sphingolipids). The x and y coordinates of the selected set of points are projected onto a plane delimited by the simulation box. This plane is subsequently divided into polygons through a Voronoi diagram using the program qvoronoi program, from the Qhull package (Barber et al.1996). Thereby, the area of each polygon is calculated.

1. Requirements

This tool assumes that the membrane under analysis is a continuous plane (e.g. no membrane pores or significant empty spaces) and that the simulations is aligned to the Z axis.
Assignments of lipids to either leaflet is based on which side of the bilayer's center of mass they happen to be. Make sure the lipids are properly wrapped in the Z direction. Extremly deformed membranes may lead also to leaflet assignment issues. Incorrect leaflet assigments may affect obtaned results.

Also, see General Requirements.

2. Input

1. Resnames: residue names defining the lipid molecules. Default values are only examples for CHARMM-GUI.
2. Atoms: atom names used in the 2D projection. Either 3 (a triad of atoms) or just 1 single atom need to be selected. Default values are only examples for CHARMM-GUI.
3. Leaflets: membrane leaflet to be analysed. “0” and “1” correspond to upper and bottom leaflets, respectively. If both are selected, an average between leaflets will be plotted in the "Area vs Frame" plot.
4. From: initial frame number.
5. To: last frame number.
6. Step: "step - 1" frames will be skipped at each iteration. One frame is analysed at each iteration.
7. Output file path: path to the output files, namely "filename_average.area" containing lipid species averages and "filename_total.area" that contains the total average area per lipid.
8. qvoronoi bynary path: path to the qhull binary. See detailed installation instructions

3. Output file format (tabulated)

filename_average.area

Lipid         Area      ResN    STD_Error    Frame Leaflet
CHL1          24.533789  66    0.762375      2  0
DOPC          58.311285   2    2.228920      2  0
DPPC          48.669009  52    0.893652      2  0
DSPC          51.244530  30    1.126525      2  0
SDPC          48.070159   2    2.332070      2  0
SM18          46.288082  48    0.661570      2  0
CHL1          26.531979  66    0.624043      2  1
DOPC          52.097192   2    2.930795      2  1
DPPC          48.406208  52    0.753630      2  1
DSPC          48.748728  30    1.140597      2  1
SDPC          46.645105   2    2.558445      2  1
SM18          45.703448  48    0.806948      2  1
CHL1          25.054534  66    0.762119      3  0
DOPC          54.538418   2    3.925157      3  0
DPPC          49.816681  52    0.788592      3  0
DSPC          50.217956  30    1.009009      3  0
SDPC          47.659967   2    0.654488      3  0
SM18          45.635846  48    0.710908      3  0
CHL1          26.497060  66    0.526496      3  1
DOPC          51.267619   2    1.974851      3  1
DPPC          48.260923  52    0.823906      3  1
DSPC          48.989282  30    1.034800      3  1
SDPC          59.614973   2    0.452165      3  1
SM18          45.743856  48    0.793890      3  1

filename_total.area

MembArea    ResN    Frame   Leaflet   BOXX        BOXY
40.609727     200        2  0     86.471794   93.925949
40.609727     200        2  1     86.471794   93.925949
40.727614     200        3  0     86.597214   94.062180
40.727614     200        3  1     86.597214   94.062180

• Lipid: residue name of each lipid species.
• Area: average area per lipid of each lipid species.
• ResN: number of residues of each lipid species.
• STD_Error: standard error of each average area per lipid. In plot versus frames, SE is the average intragrupal standard error inside each frame.
• Frame: frame number.
• Leaflet: “0” and “1” correspond to upper and bottom leaflets respectively.
• MembArea: average area per lipid of all lipid species (simulation box face area / total number of lipids).
• BOXX: simulation box X dimension.
• BOXY: simulation box Y dimension.