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Welcome to the home page of the reForge Python package.

Overview of reForge Package

The reForge source code is hosted on GitHub.

The package is primarily designed for members of the Ozkan Lab at Arizona State University, with a main focus on automating workflows for setting up, running, and analyzing all-atom or coarse-grained Molecular Dynamics (MD) simulations of biomolecular systems. The package is available to the public under the GNU GPL v3 License.

What’s in reForge?

Here are the main features of reForge:

  • Python Package for Molecular Dynamics: Provides easy-to-use workflows for setting up, running, and analyzing MD simulations of large biomolecular systems.

  • User-Friendly Interface: Designed to be accessible for both beginners and advanced users, making it easier to manage numerous MD simulations. Check out some basic workflows.

  • Optimized Mathematical Routines: Utilizes GPU and Cython acceleration to speed up analysis tasks, significantly reducing computation times.

For New Users

  • Learn the Basics: Familiarize yourself with shell scripting, SLURM, Git, and Python fundamentals.

  • Understand the Fundamentals: Develop a solid understanding of object-oriented programming and high-performance computing concepts.

  • Explore the Documentation: Browse through the available documentation and examples provided within the package to learn about the various tools and workflows available.

For Developers

  • Contribution Guidelines: If you plan to contribute to reForge, please refer to the developer documentation for coding standards, testing procedures, and version control guidelines.

  • Testing and Documentation: An extensive suite of tests and detailed documentation accompanies the package to ensure reliability and maintainability.

  • Community and Support: Contributions are welcome! Please check the GitHub repository for issues, feature requests, and further discussion.

Acknowledgements

The reForge package is maintained by DanYev. This project is inspired by and builds upon multiple excellent open-source packages such as Cython, NumPy, CuPy, GROMACS, OpenMM, Vermouth, and MDAnalysis.

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