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--- 2d_rdfs [2026/09/03 10:03] – [1) Edit Necessary Files] edit
+++ 2d_rdfs [2026/09/24 00:24] (current) – [1) Edit Necessary Files] edit
@@ Line 119: / Line 119: @@
 ====1) Edit Necessary Files====
-a) Open ''config.py'' and read the comments I left throughout. Then, adjust the fields to work for your membrane system. I would not recommend you change num_blocks (which is set at 1 by default) because it is already highly optimized and can process 20 dcds in under a minute. There's no point in trying to parallelize the workflow further.
+a) Open ''config.py'' and read the comments I left throughout. Then, adjust the fields to work for your membrane system. I would not recommend you change num_blocks (which is set at 1 by default) because it is already highly optimized and can process 20 dcds in under a minute. There's no point in trying to parallelize the workflow further. Also, custom_grouping_dict should only be modified if you have non segid MEMB lipids (check psf).
 <code>
 # Example config_dict: a complex sphingolipid membrane with some of my own custom patched NAAA lipids
@@ Line 125: / Line 125: @@
     'MEMB':['AIPE','AMPG','DPPC','CER160','CER221','LSM','BSM'],
     'NAAA':['LLL',],
+}
+# corresponding custom_grouping_dict which handles non-memb lipids like LLL, where LLL is grouped under an arbitrary label called OL
+custom_grouping_dict = {
+    'OL':['LLL'],
 }
@@ Line 131: / Line 136: @@
     'MEMB':['POPE','POPG',],
 }
-# because most of these are MEMB lipids in the psf, you don't need to specify their groupings in custom_grouping_dict
+# corresponding custom_grouping_dict which is empty since you only have normal memb lipids
+custom_grouping_dict = {
+}
 </code>