∞RETIS

Introduction

∞RETIS is a Python library designed to facilitate Replica Exchange Transition Interface Sampling (RETIS). ∞RETIS interfaces with molecular dynamics (MD) programs such as GROMACS, LAMMPS, ASE, and CP2K, offering researchers an efficient and flexible tool for advanced simulations.

Our recent publication Highly Parallelizable Path Sampling with Minimal Rejections Using Asynchronous Replica Exchange and Infinite Swaps showcases the capabilities of ∞RETIS. We are also in the process of preparing a detailed paper specifically about this software library.

Features

• Advanced Sampling Techniques: Utilizes the RETIS method and more specialized subtrajectory moves with high acceptance such as Wire Fencing for efficient sampling of rare events in molecular simulations.
• Parallel sampling: Utilizes a asynchronous replica exchange scheme for parallelization with infinite swapping.
• Seamless Integration: Easy interfacing with popular MD programs like GROMACS, LAMMPS, and CP2K. Please see the examples.

Installation

∞RETIS can be installed via pip:

pip install infretis

🚧👷 The latest development version can be installed with:

python -m pip install git+https://github.com/infretis/infretis.git@main

⚠️ Note: ∞RETIS does not manage the installation of external MD programs. Users are responsible for installing and configuring these programs independently.

Examples

We have provided several examples to help you get started with ∞RETIS:

• sugar puckering, which is an in-depth tutorial
• chignolin unfolding
• .. and much more available on the infentory repository!

Citation

If you use ∞RETIS in your research, please cite our paper: Highly Parallelizable Path Sampling with Minimal Rejections Using Asynchronous Replica Exchange and Infinite Swaps

To cite ∞RETIS in your work, please use the following BibTeX entry:

@article{zhang_highly_2024,
    title = {Highly parallelizable path sampling with minimal rejections using asynchronous replica exchange and infinite swaps},
    volume = {121},
    url = {https://www.pnas.org/doi/10.1073/pnas.2318731121},
    doi = {10.1073/pnas.2318731121},
    number = {7},
    journal = {Proceedings of the National Academy of Sciences},
    author = {Zhang, Daniel T. and Baldauf, Lukas and Roet, Sander and Lervik, Anders and van Erp, Titus S.},
    year = {2024},
    publisher = {Proceedings of the National Academy of Sciences},
}

License

∞RETIS is licensed under the MIT License. Please see the file LICENSE