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--- chain_interdigitation [2018/01/30 13:35] – edit
+++ chain_interdigitation [2026/08/17 19:44] (current) – [Interdigitation Analysis] edit
@@ Line 4: / Line 4: @@
 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.
@@ Line 11: / Line 13: @@
 Download Example: {{ :interdig-ex.tar.gz |}}
+Note: It's recommended that all users (especially those with asymmetric membranes or those with unconventional lipids) use the Modern Python Workflow inside EDP Analysis to obtain Interdigitation. That workflow can completely reproduce the results of these scripts much more efficiently - Eric Zhang.
 =====Density Calcs=====
-This section is nearly identical to EDP density calcs. The only difference lies in the //getatomnd_1.inp//
+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
+ sele resname @SEG .and. (type @TYP) .and. resid 1:100 end
 </code>
-Adjust the bolded section for how many lipids per leaflet you have
+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
+ 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**