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--- surface_area_of_lipid [2021/05/25 13:58] – admin
+++ surface_area_of_lipid [2023/02/05 10:39] (current) – admin
@@ Line 9: / Line 9: @@
 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.
-Those at UMD should use the DT2 path: **/lustre/jbklauda/scripts/area_1_lipid**
+Those at UMD should use the ZT1 path: **/afs/shell.umd.edu/project/energybio/shared/jbklauda/scripts/area_1_lipid**
 Outside of UMD a sample script is given in the gzip file: {{ :area_1_lipid.gz |}}
@@ Line 70: / Line 70: @@
 For in Fig.1, the cumulative average area (red) indicate that system reach equlibrium at around 30ns, and the areas (blue) fluctuate around the same center line, so we use the data from 50-100ns (dyn 26-50) or 60-100ns(dyn 31-50) to calculate the average area/lip. You will need to do the same for your system.
-.  Based on equilibrated dyn range on step 2, select the data points from equilibrated dyn to the end to calculate the block-average surface areas.
+. Obtaining Statistics of SA/Lipid
-.1 In 3_cal_avg_std.scr, please update the total number of last dyn*.dcd files to calculated the averages.
- <code> set Ndyn = 20 </code>
-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.
+Based on equilibrated dyn range determined in Step 2.3, select the data points from equilibrated dyn to the end to calculate the block-average surface areas.
+.1 ''3_cal_avg_std.scr''
-# This following command calculates the block average, the output file name (//area_avg_std.dat//) and the block size (1000) in time steps i.e. each dyn is treat as a block
+Update the total number of last dyn*.dcd files to calculated the averages.
-.2 Calculate the block-average surface areas by command: ''3_cal_avg_std.scr''
+ <code> set Ndyn = 20 </code>
-# Store the output file name (//area_avg_std.dat//) and the block size (# of steps in a DCD file=Ndata) in time steps into a file //area-block.inp//, which is the input data file for //area-block.exe//
+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.
-<code> echo area_avg_std.dat $Ndata > area-block.inp
-area-block.exe < area-block.inp </code>
-Note: For  //#define MAX_R 100000//  in area-block.c, you might have to change the number to a larger one (larger than your # data points) and recompile it.
-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.
+.2 Calculate the block-average surface areas by command: ''./3_calc_avg_std.scr''
-. Calculate averages, sample standard deviation, and standard error of block averages by command: ''4_run_calc_stderr.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.
-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.
+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.
-Note:
+.3 Standard Errors from Block Average
-The corresponding nanosecond are based on the "number steps" and "timestep" that we set.
-For example, in the //dyn-2.inp// file, we see  there a code line:  "numsteps            1000000           ;
-# run stops when this step is reached"
-and another code line:  <code> timestep            2.0  ;# fs/step </code>
-So you multiple 2fs/step  with 1,000,000  steps per dyn file,  which makes is 2ns per dyn file. (since 1fs=10^(-15) s, 1ns==10^(-9) s )
-==== Get the equilibrium data (test) ====
-(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):
-  area_handling.py 10 0.001 >& all.dat
-After running //pymbar_area_ka.scr//, you'll see //all.dat//, SA/lipid is in angstrom^2 and Ka is in N/m.
+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.