[[Analysis]]

======Interdigitation Analysis======

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 |}}



=====Density Calcs=====

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.


<code commend>
 sele resname @SEG .and. (type @TYP) .and. resid 1:100 end
</code>

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

Adjust in the bot directory as well

<code commend>
 sele resname @SEG .and. (type @TYP) .and. resid 101:200 end
</code>


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. 


=====Combine Densities=====

Go into thick* directories

Adjust 1_lipid_edp.scr for lipid type.

Run **1_lipid_edp.scr** and **2_comb.scr**



=====Calculate Interdigitation=====

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**