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surface_area_of_lipid

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surface_area_of_lipid [2021/05/25 14:13] – adminsurface_area_of_lipid [2023/02/05 10:39] (current) – admin
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 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.
  
-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 |}} Outside of UMD a sample script is given in the gzip file: {{ :area_1_lipid.gz |}}
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 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. 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.
  
-3.2 Calculate the block-average surface areas by command: ''./3_cal_avg_std.scr''+3.2 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. **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.
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 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.  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. 
  
-4. Calculate averages, sample standard deviation, and standard error of block averages by command: ''4_run_calc_stderr.scr''+3.3 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. 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) ==== 
- 
-(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: 
- 
-1. 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. 
- 
-2. 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)] 
-    
-3. create a conda environment and activate the env. (see conda's website for instructions) 
- 
-4. 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. 
- 
  
  
surface_area_of_lipid.1621966406.txt.gz · Last modified: 2021/05/25 14:13 by admin