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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). Calculation of SA/lipid and Ka is done automatically for your lipid only system. Make sure you run the 1_run_area.scr script from Surface Area of Lipid before doing this section. Please put the scripts listed in this wiki 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/python3.8 version for Linux [I used the '64-Bit (x86) Installer'] 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. You will likely be asked to run "conda init" at the end of the installation. If so, skip that step.
2a. 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" (The path, $HOME/anaconda3/bin, may differ depending on where Anaconda is installed, see 1c)
2b.
1) if using bash, adding "source $path_of_your_installation/anaconda3/etc/profile.d/conda.csh" as an additional line in your bashrc.mine file; 2) if using tcsh/csh, adding "source $path_of_your_installation/anaconda3/etc/profile.d/conda.csh" as an additional line in your cshrc.mine file.
Source the bashrc.mine/cshrc.mine file or just logout and login again to make these changes effective.
3. create a conda environment and activate the env. I would recommend conda's website for this (https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html). If you don't want to look it in detail. The following commands can be used:
step 1. "conda create -n geteq python=3.7 numpy"(this creates an environment called "geteq" with python 3.7 and numpy. You can give whatever evironment name to the environment.) step 2. "conda activate geteq" (this activates the environment called "geteq")
4a. Install the pymbar package.
conda install -c omnia pymbar
Ideally this should work, but not working currently (as of May 25th, 2021) due to a version mismatch issue, see below for a remedy)
4b. Install the pymbar package. (just another method)
Go to https://anaconda.org/omnia/pymbar/files → find the python3.7 version for linux → copy the link to that file, let's call it “$link” → go to anywhere in your deepthought2 account and run “wget $link” → (you should see a file named “pymbar-*.tar.bz2”) → in your activated conda environment, run “conda install pymbar-*.tar.bz2” to do a local install. This works for me as of May 25th, 2021.
Download the script: area_ka.tar.gz
Change the temperature and number of lipids per leaflet in pymbar_area_ka.scr:
temp=323.15 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.