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--- comp-sa [2026/08/23 17:51] – [Multi-lipid SA Average] edit
+++ comp-sa [2026/09/03 09:56] (current) – [Step 1: edit config.py] edit
@@ Line 7: / Line 7: @@
 Updated Authors: Yalun Yu and Jeffery Klauda\\
 Updated rtfpsf folder: Joshua Lucker \\
-Completely refactored, supports any membrane: Eric Zhang (IN PROGRESS)
+Completely refactored, supports any membrane: Eric Zhang
 All new users should use the modern Python workflow. It is highly customizable, works for any membrane system, and runs 95% faster than the legacy scripts. It has been backtested with data and reproduces numbers to 4 decimal places of accuracy compared to the legacy scripts. If there are any questions or issues with the code, reach out to ezhang32@umd.edu (may need fine-tuning).
@@ Line 167: / Line 167: @@
 Check that the system go to equilibrium by comparing the distribution data, and adjust the dyn file range when necessary. Also check the distribution, the edge is not 0, increase the area range for broader distribution.
-=====Modern Python Workflow (IN PROGRESS)=====
+=====Modern Python Workflow=====
-This workflow is designed to work for any symmetric, asymmetric membrane system. The current copy available for download has pre-defined inputs for charmms native glycerolipids, sphingolipids, sterols, and 4-5-6 chained lipid A. If you have an question, please reach out to ezhang32@umd.edu.
+This workflow is designed to work for any symmetric, asymmetric membrane system. The current copy available for download has predefined inputs for Charmm's native glycerolipids, sphingolipids, sterols, and 4-, 5-, and 6-chain lipid A. If you have a question, please reach out to ezhang32@umd.edu.
 Note: anytime you run into "no permission" issues, just run ''chmod u+x *''
@@ 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. However, if you're processing fewer than 5 dcds, I suggest you set "num_blocks = 1" because you can't parallelize the workload further. 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====
@@ Line 183: / Line 193: @@
 Next, if you left "recenter_dir = None" indicating you need to recenter your dcds, then ''recenter.scr'' will be created and you should run it using ''./recenter.scr''. This should take < 5 minutes. Otherwise, skip to the next step.
-Next, run ''1_comp_sa.scr''. This sets up a virtual Python environment and installs the MDAnalysis package before submitting the Slurm jobs. This entire process can take 1-10 minutes.
+Next, run ''./1_comp_sa.scr''. This sets up a virtual Python environment and installs the MDAnalysis package before submitting the Slurm jobs. This entire process can take 1-10 minutes.
-Finally, run ''2_analysis.py''. This computes statistics and writes txt and csv results to the ''results'' directory, which was created automatically. Here's some sample data:
+Finally, run ''./2_analysis.py''. This computes statistics and writes txt and csv results to the ''results'' directory, which was created automatically. Here's some sample data:
 <code>
 leaflet resn  N_lip  Avg_SA  Std_SA  Stderr_SA
@@ Line 223: / Line 233: @@
 Generated configuration file consumed by all downstream steps: dcd range, marker dictionary, block assignments, paths.
-**CHARMM recentering (external)**
+**CHARMM recentering**
 Recenters raw dcds so the bilayer midplane sits at z=0; output written to recenter/. Runs outside this pipeline; all downstream steps assume it has already been done.