Warning: still under active development.

This script automates the setup process for a Molecular Dynamics (MD) project, streamlining the initialization and configuration of necessary components.

• Sets up a sane default folder structure.
• Detects system information including CPU, GPU, and CUDA versions.
• Initializes Miniforge (Mambaforge) if not already set up.
• Creates a Conda environment and installs a good deal of useful packages for trajectory analysis.
• Searches and downloads starting structure files for specified proteins, from RCSPDB and/or the AlphaFold DB.
• Configures Git and sets up a complete .gitignore file.
• Runs installation tests (optional).

• Miniforge (previously Mambaforge) is recommended. You can download it from here.
• A CUDA-enabled GPU is recommended, even though the script currently does not set up GROMACS/NAMD/Amber.
• A .env file in the same directory as the script should be added, with the variables AUTHOR_NAME and AUTHOR_EMAIL.

To use the script, navigate to your project directory and run:

./initialize.sh [options]

• -t: Run tests after setting up the environment.
• -n ENVIRONMENT_NAME: Specify the name of the conda environment (default: md_project).
• -c: Use the (condaenv_cuda.yml) conda environment file which includes CUDA libraries from the Nvidia conda channel.
• -o: Install OpenMM and OpenMM-related packages.
• -h: Show the help message and exit.

./initialize.sh -t -n my_md_project

This example runs the initialization script, performs tests after setting up the environment, and specifies "my_md_project" as the conda environment name.

The script will create a series of directories to organize your MD project:

• bin: For binary files.
• src: For additional packages with source code.
• scripts: For additional scripts.
• img: For image files and plots.
• papers: For related papers and documentation.
• data: For data files, further organized into subdirectories for different stages of the MD project, excluded from git versioning.