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--- surface_area_of_lipid [2021/05/25 14:13] – admin
+++ surface_area_of_lipid [2026/09/20 00:36] (current) – refactored_scripts edit
@@ Line 3: / Line 3: @@
 ==== Overall Average SA/Lipid ====
-(authors: Xiaohong Zhuang & Jeffery Klauda)
+(authors: Xiaohong Zhuang & Jeffery Klauda)\\
+Refactored by Eric Zhang (2026)
 === Introduction ===
-This simple analysis is used to estimate the overall average surface area (SA) per lipid. If you are analyzing a single component membrane then this is equivalent to the component's SA/lipid. Otherwise, this is the average of all lipids.
+This simple analysis is used to estimate the overall average surface area (SA) per lipid. If you are analyzing a single component membrane then this is equivalent to the component's SA/lipid. Otherwise, this is the average of all lipids. UPDATE: We highly recommend using the modern Python scripts for analyses (instructions listed at the very bottom). Also, those using the modern scripts DO NOT need to run the Equilibrium Test and Area Compressibility Analyses separately (this is automatically handled).
-Those at UMD should use the DT2 path: **/lustre/jbklauda/scripts/area_1_lipid**
+Old scripts:\\
+Those at UMD should use the ZT1 path: **/afs/shell.umd.edu/project/energybio/shared/jbklauda/scripts/xiao/lipids_analyses/area_1_lipid/**\\
+Outside of UMD a sample script is given in the gzip file: {{ :area_1_lipid.gz |}}\\
+Example of analysis result in an Excel File: {{ :e.g._sa_1_lipid.xlsx |}}\\
-Outside of UMD a sample script is given in the gzip file: {{ :area_1_lipid.gz |}}
+Modern Python Scripts:\\
+{{ ::area_1_lipid_v2.tar.gz |}}
-Example of analysis result in an Excel File: {{ :e.g._sa_1_lipid.xlsx |}}
+=== Old Script Instructions ===
-=== Instructions ===
 . Copy the folder //area_1_lipid// from the path highlighted above to your directory has contains all dyn files. //area_1_lipid// should become a subdirectory of your folder with the dyn*.dcd files.
@@ Line 82: / Line 85: @@
 The example states that you want to do the averages from the last 20 dyn*dcd files. Let's say you have 50 dyn*.dcd files, then the first 30 files are ignored. If each file had 2ns of data, then you are calculating the average from 60-100ns.
-.2 Calculate the block-average surface areas by command: ''./3_cal_avg_std.scr''
+.2 Calculate the block-average surface areas by command: ''./3_calc_avg_std.scr''
 **Note: **For  //#define MAX_R 1000000//  in area-block.c, you might have to change the number to a larger one (larger than your # data points) and recompile it.
@@ Line 88: / Line 91: @@
 As you can see, the output average area data are saved in //area_avg_std.dat//. The result is given in average+- population standard deviation.
-. Calculate averages, sample standard deviation, and standard error of block averages by command: ''4_run_calc_stderr.scr''
+.3 Standard Errors from Block Average
+Calculate averages, sample standard deviation, and standard error of block averages by command: ''./4_run_calc_sterr.scr''
 The file //avg_stderr.dat// will be generated that will show the final values that we need, which are the average of the block averages and the standard error of the block averages, i.e. SA_avg/lip +- Standard error. You may refer to the attached Excel file which also demonstrate how the standard error is calculated if you are interested.
-==== Get the equilibrium data (test) ====
+==== Modern Python Script Instructions ====
+These scripts simplify and automate many of the steps in the old scripts. They also run ~10-50x faster. As mentioned earlier, they automatically check equilibrium and derive area compressibility, so you don't need the separate analysis listed elsewhere in the wiki. If there are any questions, please reach out to ezhang32@umd.edu.
-(author: Yalun Yu,  email: alanyu17@terpmail.umd.edu / yalun.research@gmail.com)
-< Email me if anything is wrong >
-This is a brief instruction to obtain the time range of equilibrium (and also the minimum block size can be used for standard error calculation). Based on these, calculation of SA/lipid and Ka is done automatically for your lipid only system. Run Xiao's //1_run_area.scr// before doing this. Please put the scripts in the same folder as you run //1_run_area.scr//. You will need pymbar package (in python) for this:
-. Install Anaconda (https://www.anaconda.com/distribution/).
-   a) Download the python3.7 version for Linux [I used the '64-Bit (x86) Installer (652.5 MB)']
-   and put the .sh installer in your home directory (or any other place you can access and execute it) on DT2.
-   b) make the .sh file an executable (chmod u+x $NameOfInstaller.sh)
-   c) Install by running "./$NameOfInstaller.sh", keep in mind where you have installed it.
-. Make sure the Anaconda installation path is included (see below) in your ~/.cshrc.mine (if using csh) or ~/.bashrc.mine (if using bash) and source the .mine file.
-   In ~/.cshrc.mine, add this line:
-   set path = ($HOME/anaconda3/bin $path)
-   or in ~/.bashrc.mine, add this line:
-   export PATH="$HOME/anaconda3/bin:$PATH" [may differ depending on where Anaconda is installed, see 1(c)]
-. create a conda environment and activate the env. (see conda's website for instructions)
-. Install the pymbar package.
-   conda install -c omnia pymbar
-Download the script: {{ :area_ka.tar.gz |}}
-Change the temperature and number of lipids per leaflet in //pymbar_area_ka.scr//:
-   set temp=323.15
-   set nlip=36
-Change the initial guess (or your preference) for block size (in ns) and the steps size (in ns) of your output (usually 1ps, but make sure to match your xst freq):
+=== Step 1: Edit ''config.py'' ===
-  area_handling.py 10 0.001 >& all.dat
+Open ''config.py''. Read the comments, then specify the number of lipids per leaflet and the path to your dyn/namd folder with dyn/dcd files.
-After running //pymbar_area_ka.scr//, you'll see //all.dat//, SA/lipid is in angstrom^2 and Ka is in N/m.
+Note: If you have an asymmetric bilayer, just let nlip = # of lipids in the top leaflet, finish the rest of the instructions, then change nlip = # of lipids in the bottom leaflet, then rerun the scripts. You'll realize that Equilibrium and Ka results don't depend on nlip.
+=== Step 2: Run Scripts ===
+Once config.py is populated, run ''./0_setup.py''. If you see error messages, just go back and fix config.py as directed and try rerunning. If system_info.txt is successfully generated, run ''./1_run_area.scr''. Once this finishes, a new results directory will appear, which contains plots and equilibirum / ka results.