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edp [2026/08/16 17:28] – [Additional Information] editedp [2026/08/27 18:29] (current) – edit
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 Updated (2023): Abhi Senthilkumar (Python scripts to automatically rename atoms and combine .sim files into xlsx)\\ Updated (2023): Abhi Senthilkumar (Python scripts to automatically rename atoms and combine .sim files into xlsx)\\
 Updated (2023): Joshua Lucker (Clarification on Step 6)\\ Updated (2023): Joshua Lucker (Clarification on Step 6)\\
-Updated (2026): Eric Zhang (Completely Refactored and Automated old scripts) IN PROGRESS\\+Updated (2026): Eric Zhang (Completely Refactored and Automated old scripts)\\
  
 Example of analysis: {{ ::e.g._thickness.xlsx |}} Example of analysis: {{ ::e.g._thickness.xlsx |}}
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 Also if there is a protein download the {{ :protein_analysis.tar |}} files and run them on as many proteins as there are in the system, and combine the data similarly to before Also if there is a protein download the {{ :protein_analysis.tar |}} files and run them on as many proteins as there are in the system, and combine the data similarly to before
 +
 +The initial instructions below are for the legacy scripts. Continue scrolling to see the updated workflow.
  
  
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 Please refer to Excel file eg_thicknesses.xlsx for the example measurement. Please refer to Excel file eg_thicknesses.xlsx for the example measurement.
  
-======Instructions Modern Python Workflow (IN PROGRESS) ======+======Instructions Modern Python Workflow ======
  
 Many of the steps in the original symmetric workflow have been combined and/or automated. This works for symmetric or asymmetric systems. It automatically computes thickness and interdigiation, so DO NOT do the separate interdigitation analysis by Eric Wang. If something isn't clear, reach out to ezhang32@umd.edu.  Many of the steps in the original symmetric workflow have been combined and/or automated. This works for symmetric or asymmetric systems. It automatically computes thickness and interdigiation, so DO NOT do the separate interdigitation analysis by Eric Wang. If something isn't clear, reach out to ezhang32@umd.edu. 
  
 ===== Step 1: Edit Necessary Files ===== ===== Step 1: Edit Necessary Files =====
-a) Open ''config.py''. Read the contents and fill in the resns list, workspace fields, and analysis fields as directed in the comments. Any patched / conjugated lipids should be entered using a tuple containing the constituent residues. Lipids uniquely identified by their segid instead of resid should also be marked using a single-element tuple. +a) Open ''config.py''. Read the comments I left in the file; they explain everything in detail. Then fill in config_dict, workspace fields, and analysis fields as directed. 
  
-Example: AIPE and AMPG are standard CHARMM lipids with segid MEMB. If I had a custom lipid composed of ORN and LLL residues, here is how I would populate ''config.py''+Example: AIPE and AMPG are standard CHARMM lipids with segid MEMB. If I had a patched lipid composed of ORN and LLL residues with segids NAAA1, NAAA2, etc., here is how I would populate ''config.py''
 <code> <code>
 # resnames should be all caps (matches case in toppar files) # resnames should be all caps (matches case in toppar files)
-resns = ['AIPE', 'AMPG', ('ORN','LLL'),] # conform to Python syntax by surrounding strings with double or single quotes+config_dict = { 
 +    'MEMB':{ 
 +        'AIPE': (58.3686, 58.2105), 
 +        'AMPG': (61.0204, 59.9090), 
 +    }, 
 +    'NAAA':{ # for patched / conjugated lipid, set subresidues to have the same comp_sa 
 +        'ORN': (52.8182, 52.8821), 
 +        'LLL': (52.8182, 52.8821), 
 +    }, 
 +    'IONS': { 
 +        'POT': None, 
 +        'CLA': None, 
 +    }, 
 +    'TIP3':{ 
 +        'TIP3': None, 
 +    }, 
 +}
 </code> </code>
  
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 c) Now run ''./0_setup.py''. Confirm that all files are generated successfully before continuing. c) Now run ''./0_setup.py''. Confirm that all files are generated successfully before continuing.
  
-===== Step 2:Automatically Get EDP Data =====+===== Step 2: Automatically Get EDP Data =====
  
-a) Run ''./1_recenter.scr''. This should take <5 minutes. Confirm that you have recentered dcds in your recenter directory after the job finishes.+a) If you set recenter_dir = None in config.py, you will see a new recenter script and a directory be created. If not, skip to the next step. Run ''./recenter.scr''. This should take <5 minutes. Confirm that you have recentered the dcds in your recenter directory after the job finishes.\\
  
-b) Run ''./run_edp.scr''. This completely automates steps 2-7 of the edp pipeline. You should see printed output explaining which steps are running. It will take <2 minutes. If everything went smoothly, you're essentially done! You can continue modifying plots by examining the comments in ''6_plot_edp.py'' or directly tweaking the code in ''src/plot_params.py''. If you set EXP_format = True in ''config.py'', you'll see a new directory called SimToEXP which contains the formatted files required for SimToEXP software. Details about the usage for SimToEXP are covered in Part V of the legacy scripts above, and it's not necessary for most. The results folder contains EDP_results.txt, which holds thickness and interdigitation results plus any plots.  
  
-Note: If you want to rerun steps individually, just run the numbered .scr or .py scripts. Verify that your lipids are assigned to the correct leaflet based on printed output or by checking ''memb_compositon.csv'' inside the sim_data folder.+b) Run ''1_atm_dens.scr''. The first time you run it, it will take a couple of minutes to set up a virtual environment with the MDAnalysis package installed. Then, it will automate all other steps and run for < 1 minute. You should now see the default plots, thickness data, and interdigitation data in the results folder. If you need NSLD data, all of the formatted .sim and .cmp files can be found inside the SimToEXP folder. Read more about SimToEXP in part VI of the legacy script instructions.
  
 ===== Additional Information ===== ===== Additional Information =====
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 === Overall Pipeline === === Overall Pipeline ===
- + 0_setup.py roughly validates the structure of all the fields in config.py before generating necessary files. 1_atm_dens.scr create a virtual Python environment, then runs 1_atm_dens.py to get .sim files with atom densities -> 2_calc_edp.py which applies the electron weights and groups atoms according to the .cmp files -> 3_analysis.py which computes thickness and interdigitation data -> 4_plot_edp.py which creates generic plots based on the edp data -> 5_exp_format.py which formats .cmp and .sim files to be usable in SimToEXP.
-  - **Edit ''config.py''** — resns list, charmm_dir, dyn_dir, dcd_range, bilayer_only, save_csv, EXP_format, charmm_version, job_time_limit +
-  - **''0_setup.py''** — validates config, generates ''recenter_vars.str'', ''toppar_temp.str'', ''recenter.csh'', ''system_info.txt''; creates subdirs +
-  - **''1_recenter.scr''** — submits ''recenter.csh'' (3-pass CHARMM recentering) -> recentered DCDs +
-  - **''2_run_gen_rtf.scr''** — atom labels + group classification (via ''atmlbl.py''/''cmp.py'') -> ''atmlbl_cmp_files/'' +
-  - **''3_bldsim.py''** — per-atom, per-leaflet density from DCDs -> ''sim_data/'' +
-  - **''4_calc_edp.py''** — electron weighting + group EDP -> ''edp_data/'' +
-  - **''5_analysis.py''** — thickness (DHH/DB/2DC) + interdigitation -> ''results/EDP_results.txt'' +
-  - **''6_plot_edp.py''** — EDP plots -> ''results/*.png'' +
-  - **''7_exp_format.py''** — SimToEXP formatting, only if ''EXP_format = True'' -> ''SimToEXP/'' +
- +
-=== Comparison with the Legacy Scripts === +
-Pros:  +
-The legacy scripts only worked for symmetric bilayers involving some glycero and sphingo lipids. It also used nested loop structures to get z-coordinate data for all atoms in the simulation, whereas this script directly greps the dcds, turning a 1-6 hour job into a 30-second job.  +
- +
-Cons: +
-The plotting scripts are already heavily customized. For those not comfortable with Python and Matplotlib, it may be easier to import *.dat files with edp data into Excel as CSV files and plot there, or use any alternative software. (Removed old generate Excel script because all *.dat files are already in CSV format, which is easily read into Excel).+
  
 === How to Interpret Last 2 Columns in Thickness Results ====== === How to Interpret Last 2 Columns in Thickness Results ======
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 === Formulas for Self and Hetero Interdigitation === === Formulas for Self and Hetero Interdigitation ===
- +{{:new_interdig_formulas.png}}
-Overall System Self-Interdigitation +
-''I<sub>self, overall</sub> = ∫ [ 4 · ρ<sub>top</sub>(z) · ρ<sub>bot</sub>(z) / (ρ<sub>top</sub>(z) + ρ<sub>bot</sub>(z))² ] dz'' +
- +
-Homo (Self) Lipid Interdigitation +
-''I<sub>self, i</sub> = ∫ [ 4 · ρ<sub>i,top</sub>(z) · ρ<sub>i,bot</sub>(z) / (ρ<sub>i,top</sub>(z) + ρ<sub>i,bot</sub>(z))² ] dz'' +
- +
- Hetero Lipid Interdigitation (best for asymmetric systems) +
-''I<sub>top, i</sub> = ∫ [ 4 · P<sub>i,top</sub>(z) · P<sub>bot, tails</sub>(z) / (P<sub>i,top</sub>(z) + P<sub>bot, tails</sub>(z))² ] dz'' +
- +
-''I<sub>bot, i</sub> = ∫ [ 4 · P<sub>i,bot</sub>(z) · P<sub>top, tails</sub>(z) / (P<sub>i,bot</sub>(z) + P<sub>top, tails</sub>(z))² ] dz'' +
- +
-Where normalized probability density is: +
-''P(z) = ρ(z) / ∫ ρ(z) dz'' +
edp.1786915692.txt.gz · Last modified: 2026/08/16 17:28 by edit