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...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.展开更多
The percolation threshold(PT)for colloidal system refers to the point at which particles aggregate to form an infinite cluster that spans the suspension[1].It is widely assumed that the percolation transition should f...The percolation threshold(PT)for colloidal system refers to the point at which particles aggregate to form an infinite cluster that spans the suspension[1].It is widely assumed that the percolation transition should follow the concept of scaling,and recent numerical studies[2-5]have shown that the wrapping probability of percolation can be described by the universal scaling functions,which enables the estimation of PTs for different types of system.展开更多
基金the National Key R&D Program of China(2017YFA0204702)the National Natural Science Foundation of China(21821004,21873007 and 21927901)CAAI-Huawei MindSpore Open Fund for financial support.
文摘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.
基金supported by the National Natural Science Foundation of China(Grant Nos. 11602279,11232013,and 11472285)
文摘The percolation threshold(PT)for colloidal system refers to the point at which particles aggregate to form an infinite cluster that spans the suspension[1].It is widely assumed that the percolation transition should follow the concept of scaling,and recent numerical studies[2-5]have shown that the wrapping probability of percolation can be described by the universal scaling functions,which enables the estimation of PTs for different types of system.
