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2d_rdfs [2026/08/26 16:41] – [2) Run Scripts] edit2d_rdfs [2026/09/24 00:24] (current) – [1) Edit Necessary Files] edit
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 ====1) Edit Necessary Files==== ====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). 
-Example config_dict: a complex sphingolipid membrane with some of my own custom patched NAAA lipids+
 <code> <code>
 +# Example config_dict: a complex sphingolipid membrane with some of my own custom patched NAAA lipids
 config_dict = { config_dict = {
     'MEMB':['AIPE','AMPG','DPPC','CER160','CER221','LSM','BSM'],     'MEMB':['AIPE','AMPG','DPPC','CER160','CER221','LSM','BSM'],
     'NAAA':['LLL',],     'NAAA':['LLL',],
 } }
-# because most of these are MEMB lipids in the psf, you don't need to specify their groupings in custom_grouping_dict + 
-# FYI, the default MEMB groupings are for CHL, PE, PG, PC, PI, PS, PA, CER, SM lipids; other native MEMB lipids need manual code adjustment+# 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'], 
 +} 
 + 
 +# Example of a simple POPE/POPG membrane which have segid MEMB because they are native lipids 
 +config_dict = { 
 +    'MEMB':['POPE','POPG',], 
 +} 
 + 
 +# corresponding custom_grouping_dict which is empty since you only have normal memb lipids 
 +custom_grouping_dict = { 
 +}
 </code> </code>
  
2d_rdfs.1787776891.txt.gz · Last modified: 2026/08/26 16:41 by edit