LipidInterdigitation

Lipid interdigitation

This tool computes three measures of lipid interdigitation:

1. Fraction of mass overlap (or mass distribution correlation, 0 < Iρ < 1;
2. Width of the region of mass overlap, w_ρ, only defined if Iρ > 0;
3. Fraction of inter-leaflet atomic contacts, 0 < Ic < 1.

Specifically, ; w_ρ is the second central moment of ρ_a ρ_b; and Ic is built by counting the number of atoms that are in contact with the opposite leaflet.

Please refer to the MEMBPLUGIN paper in Bioinformatics, doi:10.1093/bioinformatics/btu037 (bioinformatics.oxfordjournals.org), for the details.

1. Requirements

See [GeneralRequirements].

2. Input

1. Atom selection: atoms to include in the analysis. Default: "membplugin_lipids and noh".
2. Analyze slab min: minimum Z for the analysis. Atoms whose z coordinate falls below this value will not be considered. Use min to include the whole system.
3. Analyze slab max: maximum Z for the analysis, as above. Use max to include the whole system.
4. Resolution: grid spacing used to compute mass densities.
5. Bilayer center: reference coordinate used to assign molecules to either leaflet, or auto (use the bilayer's geometrical center).
6. Cut-off distance: for contacts-based interdigitation, the distance below which atoms are considered in contact.
7. From: initial frame number.
8. To: last frame number. To analyze until the last frame, type “last”.
9. Step: "step - 1" frames will be skipped at each iteration. One frame is analysed at each iteration.
10. Output file path: path to the output files that will be created. A file suitable for external analysis called filename.interdigitation will be created.

3. Output file format (tabulated)

filename.interdigitation

Frame  CorrelFrac  CorrelWidth   ContactFrac ContactN
0       0.15811    3.38069   0.02485   432
1       0.12590    3.04812   0.02663   463
2       0.14174    2.80659   0.02266   394
3       0.12666    3.53090   0.02261   393
4       0.12590    2.80682   0.02646   460
5       0.13441    3.00746   0.02623   456
6       0.12306    2.75611   0.02520   438
7       0.13168    2.98283   0.02692   468
8       0.13758    2.91784   0.02502   435
9       0.13233    3.02087   0.02462   428
[...]

• Frame: frame number.
• CorrelFrac: Fraction of mass overlap (or mass distribution correlation, 0 < Iρ < 1;
• CorrelWidth: Width of the region of mass overlap, w_ρ, only defined if Iρ > 0;
• ContactFrac: Fraction of inter-leaflet atomic contacts, 0 < Ic < 1.
• ContactN: Number of inter-leaflet atomic contacts.