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--- comp-sa [2026/08/25 17:21] – [Step 1: edit config.py] edit
+++ comp-sa [2026/09/03 09:56] (current) – [Step 1: edit config.py] edit
@@ Line 174: / Line 174: @@
 ====Step 1: edit config.py====
-Open ''config.py''. Read the comments carefully and fill in the specified fields. As mentioned in the file, you probably don't need to touch fields in the last section. For patched lipids, only add the subresidues that have marker atoms. You also do not need to specify how many lipids are in each leaflet; that is automatically determined at runtime.
+Open ''config.py''. Read the comments carefully and fill in the specified fields. As mentioned in the file, you probably don't need to touch fields in the last section, but you have to change config_dict, dyn_dir, charmm_dir, and dcd_range. The dcd_range should be the equilibrated dcd range you found from the geteq analysis. You also do not need to specify how many lipids are in each leaflet; that is automatically determined at runtime. 90% of users don't need to worry about this, but for those working with patched lipids, add only the subresidues with marker atoms.
+I embedded a lot of error handling in the scripts, so don't worry too much about precision if something isn't clear.
+Example Membrane with just POPE/POPG lipids (which have segid MEMB since they are part of CHARMM's native lipid library).
+<code>
+config_dict = {
+    'MEMB':['POPE','POPG',],
+}
+# ignore the current config_dict in the files with lipids like 'AIPE' and 'LLL'; that's specific to the membranes I was working with at the time when developing the scripts.
+</code>
-I embedded lots of error handling into the scripts, so don't worry too much about being precise if something isn't clear.
 ====Step 2: run scripts====