Author: Eric Wang

Please email me at ericzwang@gmail.com if something isn't clear

This instruction is very similar to EDP because it relies on density profiles. I removed recentering from this analysis to save space. Add it in if you haven't done EDP.

Download Script: interdig-script.tar.gz
Download Example: interdig-ex.tar.gz

This section is nearly identical to EDP density calcs.

The recentered dcds are loaded in from the EDP section. One difference lies in the getatomnd_1.inp which selects for each leaflet.

 sele resname @SEG .and. (type @TYP) .and. resid 1:100 end

Adjust resid 1:100 for how many lipids per leaflet you have

Adjust in the bot directory as well

 sele resname @SEG .and. (type @TYP) .and. resid 101:200 end

Also, I was using a FFA which is not in the library. In this case, I created my own *.cmp file and renamed it to *.cmp2. I then copied the .cmp2 file to .cmp and used it for density calcs.

Go into thick* directories

Adjust 1_lipid_edp.scr for lipid type.

Run 1_lipid_edp.scr and 2_comb.scr

Go to interdig directory

Adjust inter.m for how many lipid types you have. This file takes the densities, constructs overlap density, and integrates to get interdigitation parameter. The formula for overlap density can be found in Das et al. Biophysical Journal 2009, 97 (7), 1941-1951.

Type ./inter.csh to run inter.m

The final parameters are in int.dat and the overlap profiles are in profile.dat