This repository contains the files for the molecular simulation workshop at the Max-Planck-Institut für Polymerforschung, Mainz, Germany as part of the CECAM workshop for FAIR and TRUE simulations on September 28, 2023
Authors: Eliseo Marin, Ryan DeFever and Edward Maginn
The following computer setup instructions are heavily based on the Molecular Sciences Software Institute workshop materials for software development best practices.
In preparation for this workshop, you will need to have the MoSDeF set of tools, which include mBuild, Foyer, mosdef_cassandra installed on your computer.
This workshop will require the use of the Python programming language and many libraries that are available in that ecosystem. One of the easiest ways to get started with Python, its libraries and molecular simulation software, is via the conda package manager. You can get access to these tools via Anaconda or Miniconda.
Anaconda is a distribution of Python, the conda package manager, and several third-party libraries which are commonly used in data science. Miniconda contains only Python and the conda package manager. You will be able to install any package you would like later using miniconda. Miniconda will take up a lot less space on your computer. We will be using conda environments and install the packages we need, so we consider miniconda to be the better option between the two. If you already have Anaconda installed, however, there is no need to install miniconda. If you have previously installed anaconda or miniconda in your machine, feel free to skip to the section Setting up conda environments.
It is strongly recommended that Windows users install the Windows Subsystem for Linux (WSL) in advance. You should install WSL2 and have Windows 10 or 11 in your local machine. If you have an older version of Windows, please contact the workshop organizers.
The instructions for installing WSL2 can be found in the official Windows documentation. If you do not have a preference on Linux distribution, we recommend installing Ubuntu.
Once WSL2 is installed, open your “Start” menu and choose “Ubuntu”. This will open a terminal window. You may see a message about finishing the installation. After the installation is done, you will have to create a username and password. After this, you should be able to use the terminal.
WSL2 is like having a Linux distribution inside your Windows machine. You can run Linux programs and Windows programs simultaneously. You can access files from Linux from Windows and vice versa. For more information, we recommend reading the excellent WSL2 documentation.
The instructions after this section need to be entered in the terminal.
The installers for miniconda can be obtained from the download section of the conda website. Below we provide the instructions for convenience.
Open the terminal and download the miniconda scripts from the terminal. If you use Linux or WSL
If you do not have curl already installed:
> sudo apt-get install curl
Otherwise, you can skip the latter step.
> curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
> bash Miniconda3-latest-Linux-x86_64.sh
Follow the instructions. After the installation is complete, close and open the terminal. You should see a (base) before your username in the command line. Please type
> conda init
If you use MacOS, please go to the website and pick the appropriate installer for your computer architecture. If you have a newer Mac with an M1 processor, please do:
> curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-arm64.sh
> bash Miniconda3-latest-MacOSX-arm64.sh
If you have an x86 architecture (Intel):
> curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
> bash Miniconda3-latest-MacOSX-x86_64.sh
Follow the instructions. After the installation is complete, close and open the terminal. You should see a (base) before your username in the command line. Please type
> conda init
Before we start, we need to add conda-forge to the channels available to our conda installation. Conda channels are the locations of the libraries and programs that we will be using. Conda-forge is a channel that contains many packages that are frequently used in fields such as molecular simulations or data science. These packages are maintained by the developers and are relatively up to date.
Conda-forge does not come as a default package in conda, so we need to add it first
> conda config --add channels conda-forge
> conda config –-set channel_priority strict
Optional and suggested: you might want to install mamba, a C++ reimplementation of conda. This will make it fast to install the required packages. Install mamba in the base environment as:
> conda install mamba -n base -y
This may take several minutes to complete - be patient.
You are now ready to create the conda environments that we will need for the workshop. We will create the conda environment required to run this workshop. If you did NOT install mamba, type:
> conda create -n cassandra-tutorial mosdef_cassandra matplotlib jupyter garnett pycifrw jupyter -y
Alternatively, if you decided to install mamba in the base environment:
> mamba create -n cassandra-tutorial mosdef_cassandra matplotlib jupyter garnett pycifrw jupyter -y
You can test the second environment:
> conda activate cassandra-tutorial
> python -c “import mosdef_cassandra”
> cassandra.exe
You can alter between environments freely using the following command:
> conda activate cassandra-tutorial
To return to “base” use:
> conda deactivate
Clone this GitHub repository by doing
> git clone https://github.com/maginngroup/cecam-workshop
Navigate to the root directory and do
> jupyter notebook
Select the notebook that you would like to explore and have fun!