SPONGE (Simulation Package tOward Next GEneration molecular modeling) is a software package for molecular dynamics (MD) simulation of solution and surface molecular systems. In this version of SPONGE, the all- atom potential energy functions used in AMBER MD packages are used by default and other all-atom/coarse- grained potential energy functions are also supported. SPONGE is designed to extend the timescale being approached in MD simulations by utilizing the latest CUDA- enabled graphical processing units (GPU) and adopting highly efficient enhanced sampling algorithms, such as integrated tempering, selective integrated tempering and enhanced sampling of reactive trajectories. It is highly modular and new algorithms and functions can be incorporated con veniently. Particularly, a specialized Python plugin can be easily used to perform the machine learning MD simulation with MindSpore, TensorFlow, PyTorch or other popular machine learning frameworks. Furthermore, a plugin of Finite-Element Method (FEM) is also available to handle metallic surface systems. All these advanced features increase the power of SPONGE for modeling and simulation of complex chemical and biological systems.

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SPONGE：具有增强采样和 AI 驱动算法的 GPU 加速分子动力学包

SPONGE（面向下一代分子建模的模拟包）是用于溶液和表面分子系统的分子动力学（MD）模拟的软件包。在这个版本的 SPONGE 中，默认使用 AMBER MD 包中使用的全原子势能函数，也支持其他全原子/粗粒势能函数。SPONGE 旨在通过利用最新的支持 CUDA 的图形处理单元 (GPU) 并采用高效的增强采样算法（例如集成回火、选择性集成回火和反应轨迹的增强采样）来延长 MD 模拟中接近的时间尺度。它是高度模块化的，可以方便地集成新的算法和功能。特别，一个专门的 Python 插件可以很容易地使用 MindSpore、TensorFlow、PyTorch 或其他流行的机器学习框架来执行机器学习 MD 模拟。此外，还可以使用有限元方法 (FEM) 插件来处理金属表面系统。所有这些高级功能都增强了 SPONGE 对复杂化学和生物系统进行建模和模拟的能力。