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--- chain_interdigitation [2018/01/30 13:46] – 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.
@@ Line 22: / Line 27: @@
 </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
@@ Line 44: / Line 49: @@
-=====Combine Densities=====
+=====Calculate Interdigitation=====
-Go out into interdig directory
+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 <code commend>
+Type ''./inter.csh'' to run inter.m
- ./inter.csh
-</code>
+The final parameters are in **int.dat** and the overlap profiles are in **profile.dat**