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Setting_up_an_OSX_Computer.md

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Welcome!!!

  1. First things first, let's install Homebrew, the missing package for macOS! This will make our lives a lot easier when trying to install other things later. Run the below command

    /usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

    If you are having issues with Homebrew or something isn't downloading correctly, brew doctor is a great command to check and see what is going on. You may also need to do brew upgrade if things still aren't working.

  2. Now install some much needed packages!

    brew install git make build-essential rlwrap wget

  3. Since git is installed now, clone cmeutils and getting-started from GitHub since they have important settings that we use to run our simulations and code.

    This part is more optional than required but our getting_started config_files folder has some defaults already set up for your bash_profile, vmdrc (which you will download in a moment), and vimrc and you can follow the below commands to copy them into your own files.

    cd getting-started/config_files/
make

  4. Install VMD! (If you're running OSX Catalina, use this VMD.) Then install the gsd-vmd plugin which allows you to visualize the gsd files we make when running simulations:

    git clone https://github.com/mphoward/gsd-vmd
cd gsd-vmd

    Catalina users only change line 18 in the file CMakeLists.txt from

    set(CMAKE_OSX_ARCHITECTURES "i386;x86_64" CACHE STRING "Build architectures for OSX" FORCE) to

    set(CMAKE_OSX_ARCHITECTURES "x86_64" CACHE STRING "Build architectures for OSX")

    mkdir build && cd build
cmake ..
make install

  5. Download Miniconda! For more extensive instructions, visit the Installing the Frequently-Used Programs for CME-Lab tab in the getting-started wiki.

    cd Downloads/
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
bash Miniconda3-latest-MacOSX-x86_64.sh

    Now we can install programs with conda!

    RECOMMENDED: Create conda environments to reflect what you want each of them to do.

    conda create --name <new environment name> --> creates a new environment
    conda activate <environment name> --> puts you in your environment
    conda deactivate --> takes you out of your environment
    conda env remove -n <environment name> --> removes an environment
    conda create --name <new environment name> --clone <the one you are cloning> --> copies one environment into another

NOTE: If you haven't used vim before as an editor, you can do a tutorial with the command vimtutor which will help you understand how to type in files!