Free Energy Simulations with the AMOEBA Polarizable Force Field and Metadynamics on GPU Platform
Zhang, Yuebin; Li, Guohui; Peng, Xiangda; Chu, Huiying
刊名JOURNAL OF COMPUTATIONAL CHEMISTRY
2016-03-05
卷号37期号:6页码:614-622
关键词Amoeba Polarizable Force Field Metadynamics Gpu Acceleration Free Energy Simulations Openmm Plumed Alanine Dipeptide Water Simulation
ISSN号0192-8651
DOI10.1002/jcc.24227
文献子类Article
英文摘要The free energy calculation library PLUMED has been incorporated into the OpenMM simulation toolkit, with the purpose to perform enhanced sampling MD simulations using the AMOEBA polarizable force field on GPU platform. Two examples, (I) the free energy profile of water pair separation (II) alanine dipeptide dihedral angle free energy surface in explicit solvent, are provided here to demonstrate the accuracy and efficiency of our implementation. The converged free energy profiles could be obtained within an affordable MD simulation time when the AMOEBA polarizable force field is employed. Moreover, the free energy surfaces estimated using the AMOEBA polarizable force field are in agreement with those calculated from experimental data and ab initio methods. Hence, the implementation in this work is reliable and would be utilized to study more complicated biological phenomena in both an accurate and efficient way. (C) 2015 Wiley Periodicals, Inc.
WOS关键词MOLECULAR-DYNAMICS SIMULATIONS ; ORTHOGONAL SPACE ; RANDOM-WALK ; PROTEINS ; MODEL ; BIOMOLECULES ; SYSTEMS ; WATER
WOS研究方向Chemistry
语种英语
出版者WILEY-BLACKWELL
WOS记录号WOS:000370254600009
内容类型期刊论文
源URL[http://cas-ir.dicp.ac.cn/handle/321008/171252]  
专题大连化学物理研究所_中国科学院大连化学物理研究所
通讯作者Li, Guohui
作者单位Chinese Acad Sci, Dalian Inst Chem Phys, State Key Lab Mol React Dynam, Lab Mol Modeling & Design, 457 Zhongshan Rd, Dalian 116023, Peoples R China
推荐引用方式
GB/T 7714
Zhang, Yuebin,Li, Guohui,Peng, Xiangda,et al. Free Energy Simulations with the AMOEBA Polarizable Force Field and Metadynamics on GPU Platform[J]. JOURNAL OF COMPUTATIONAL CHEMISTRY,2016,37(6):614-622.
APA Zhang, Yuebin,Li, Guohui,Peng, Xiangda,&Chu, Huiying.(2016).Free Energy Simulations with the AMOEBA Polarizable Force Field and Metadynamics on GPU Platform.JOURNAL OF COMPUTATIONAL CHEMISTRY,37(6),614-622.
MLA Zhang, Yuebin,et al."Free Energy Simulations with the AMOEBA Polarizable Force Field and Metadynamics on GPU Platform".JOURNAL OF COMPUTATIONAL CHEMISTRY 37.6(2016):614-622.
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