PyRETIS 3: Conquering rare and slow events without boundaries,Journal of Computational Chemistry

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PyRETIS 3: Conquering rare and slow events without boundaries
Journal of Computational Chemistry ( IF 3.4 ) Pub Date : 2024-02-12 , DOI: 10.1002/jcc.27319
Wouter Vervust ₁ , Daniel T Zhang ₂ , An Ghysels ₁ , Sander Roet ₃ , Titus S van Erp ₂ , Enrico Riccardi ₄

Affiliation

We present and discuss the advancements made in PyRETIS 3, the third instalment of our Python library for an efficient and user-friendly rare event simulation, focused to execute molecular simulations with replica exchange transition interface sampling (RETIS) and its variations. Apart from a general rewiring of the internal code towards a more modular structure, several recently developed sampling strategies have been implemented. These include recently developed Monte Carlo moves to increase path decorrelation and convergence rate, and new ensemble definitions to handle the challenges of long-lived metastable states and transitions with unbounded reactant and product states. Additionally, the post-analysis software PyVisa is now embedded in the main code, allowing fast use of machine-learning algorithms for clustering and visualising collective variables in the simulation data.

中文翻译：

PyRETIS 3：无边界地征服罕见且缓慢的事件

我们介绍并讨论 PyRETIS 3 中取得的进步，这是我们的 Python 库的第三部分，用于高效且用户友好的罕见事件模拟，重点是通过副本交换过渡界面采样 (RETIS) 及其变体执行分子模拟。除了对内部代码进行总体重新布线以实现更加模块化的结构之外，还实施了一些最近开发的采样策略。其中包括最近开发的蒙特卡罗举措，以提高路径去相关性和收敛速度，以及新的系综定义，以应对长期亚稳态和无界反应物和产物状态转变的挑战。此外，后分析软件 PyVisa 现在嵌入到主代码中，允许快速使用机器学习算法对模拟数据中的集体变量进行聚类和可视化。

更新日期：2024-02-12

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