SPONGE
SPONGE 是面向高性能分子模拟的核心程序，支持分子动力学、增强采样、自由能计算以及多硬件平台加速。
SPONGE: A GPU-Accelerated Molecular Dynamics Package with Enhanced Sampling and AI-Driven Algorithms DOI: 10.1002/cjoc.202100456SPONGE 面向下一代分子科学的分子模拟软件
SPONGE 由北京大学高毅勤课题组开发，在高性能分子动力学、增强采样、自由能计算与 AI 增强分子模拟等方向持续推进。
如何引用
如果 SPONGE 及相关工具支持了你的研究工作，请在论文中引用对应的软件或方法论文。
MindSPONGE
MindSPONGE是通过Mindspore神经网络框架编写的AI增强的SPONGE分支。
Artificial Intelligence Enhanced Molecular Simulations DOI: 10.1021/acs.jctc.3c00214Xponge
使用 Python 编写的分子动力学模拟前后处理工具。
Xponge: A Python package to perform pre- and post-processing of molecular simulations DOI: 10.21105/joss.04467代表性研究成果
2025
A Sinking Approach to Explore Arbitrary Areas in Free Energy Landscapes
DOI: 10.1021/jacsau.5c00460
2024
Integrating Epigenetics, Proteomics, and Metabolomics to Reveal the Involvement of Wnt/β-Catenin Signaling Pathway in Oridonin-Induced Reproductive Toxicity
DOI: 10.3390/toxics12050339
2024
PMC-IZ: Electrostatics Calculation in Slab Geometric Molecular Dynamics Simulations
DOI: 10.1021/acs.jctc.3c01124
2023
Nanoscale one-dimensional close packing of interfacial alkali ions
DOI: 10.1038/s41565-023-01550-9
2023
Investigating the Activation Mechanism Differences between Human and Mouse cGAS
DOI: 10.1021/acs.jpcb.3c02377
2023
High Li+ coordinated solvation sheaths enable high-quality Li metal anode
DOI: 10.1002/inf2.12411
2023
Effect of stereoregularity on excitation-dependent fluorescence and room-temperature phosphorescence of poly(2-vinylpyridine)
DOI: 10.1002/agt2.276
2023
Action at a distance: organic cation induced long range organization of interfacial water enhances hydrogen evolution and oxidation kinetics
DOI: 10.1039/D3SC03300G
发展脉络
2026
SPONGE 2.0 进入 beta 测试，面向新一代分子模拟工作流持续完善
2024
发布 SPONGE 1.4 正式版本，继续扩展模拟功能与文档体系
2023
发布 SPONGE 1.3，推进增强采样、自由能计算与应用示例建设
2021