Release Notes

Below is a summary of recent changes for both NERDSS and ionerdss. For more detailed commit history, please see the respective GitHub repositories.

NERDSS

  • New Website

    A dedicated NERDSS site is now live at https://mjohn218.github.io/NERDSS/

  • NERDSS v1.2.1 (Mar 22, 2025)

    This release addresses the loop closure issue that occurs when reaction rates are high.

  • Parallel NERDSS v1.0.0 (Dec 2024)

    A parallelized version of NERDSS is available to speed up simulations on multiple processors. For more information, visit the NERDSS MPI branch on GitHub.

ionerdss

  • Version 1.1.0 (Mar 22, 2025)

    • Refactored the code into model, nerdss_simulation, and nerdss_analysis modules.

    • Unified figure plotting with the plot_figure() function in the analysis class.

    • Added the ability to visualize model structure compared with PDB structure in Jupyter Notebooks using PyMOL.

    • Added the ability to visualize trajectories in Jupyter Notebooks using OVITO.

    • The previous unrefactored functions are retained in the analysis and model_setup modules for backward compatibility.

  • Version 1.0.37 (Mar 7, 2025)

    • This release introduces a new feature to regularize homo chains in PDB structures to the same NERDSS molecule type.

  • Version 1.0.36 (Jan 23, 2025)