典型文献
SPONGE:A GPU-Accelerated Molecular Dynamics Package with Enhanced Sampling and Al-Driven Algorithms
文献摘要：
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.
文献关键词：
中图分类号：
作者姓名：
Yu-Peng Huang;Yijie Xia;Lijiang Yang;Jiachen Wei;Yi Isaac Yang;Yi Qin Gao
作者机构：
College of Chemistry and Molecular Engineering,Peking University,Beijing 100871,China;Beijing National Laboratory for Molecular Sciences,Peking University,Beijing 100871,China;Biomedical Pioneering Innovation Center,Peking University,Beijing 100871,China;Beijing Advanced Innovation Center for Genomics,Peking University,Beijing 100871,China;State Key Laboratory of Nonlinear Mechanics and Beijing Key Laboratory of Engineered Construction and Mechanobiology,Institute of Mechanics,Chinese Academy of Sciences,Beijing 100190,China;Shenzhen Bay Laboratory,Gaoke Innovation Center,Guangqiao Road,Guangming District,Shenzhen,Guangdong 518132,China
文献出处：
引用格式：
[1]Yu-Peng Huang;Yijie Xia;Lijiang Yang;Jiachen Wei;Yi Isaac Yang;Yi Qin Gao-.SPONGE:A GPU-Accelerated Molecular Dynamics Package with Enhanced Sampling and Al-Driven Algorithms)[J].中国化学（英文版）,2022(01):160-168
A类：
SPONGE,tOward,GEneration,AMBER,proached,veniently
B类：
GPU,Accelerated,Molecular,Dynamics,Package,Enhanced,Sampling,Driven,Algorithms,Simulation,Next,molecular,modeling,software,dynamics,MD,solution,surface,systems,In,this,version,atom,potential,energy,functions,used,packages,by,default,other,coarse,grained,also,supported,designed,extend,timescale,being,simulations,utilizing,latest,CUDA,enabled,graphical,processing,units,adopting,highly,efficient,enhanced,sampling,algorithms,such,integrated,tempering,selective,reactive,trajectories,It,modular,new,can,corporated,con,Particularly,specialized,thon,plugin,easily,perform,machine,learning,MindSpore,TensorFlow,PyTorch,popular,frameworks,Furthermore,Finite,Element,Method,FEM,available,handle,metallic,All,these,advanced,features,increase,power,complex,chemical,biological
AB值：
0.554462
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