Free Energy Simulations with the AMOEBA Polarizable Force Field and Metadynamics on GPU Platform

doi:10.1002/jcc.24227

	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
DOI	10.1002/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.