SPONGE:A GPU-Accelerated Molecular Dynamics Package with Enhanced Sampling and Al-Driven Algorithms

• 作者: Yu-Peng Huang Yijie Xia Lijiang Yang Jiachen Wei Yi Isaac Yang Yi Qin Gao
• 来源期刊: 中国化学（英文版）
• 年，卷（期）: 2022,（1）
• 所属期刊栏目: Chemistry Authors Up Close
• 页码范围: 160-168
• 页数: 9页
• 语种: 英文
• DOI: 10.1002/cjoc.202100456

摘要

SPONGE (Simulation Package tOward Next GEneration molecular modeling) is a software package for molecu-lar 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 ap-proached 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 in-corporated con veniently.Particularly,a specialized Py-thon 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.