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Integrating Multiple Accelerated Molecular Dynamics To Improve Accuracy of Free Energy Calculations

文献类型：期刊论文

作者Peng, Xiangda1,2; Zhang, Yuebin1; Li, Yan1; Liu, QingLong1; Chu, Huiying1; Zhang, Dinglin1; Li, Guohui1
刊名JOURNAL OF CHEMICAL THEORY AND COMPUTATION
出版日期2018-03-01
卷号14期号:3页码:1216-1227
ISSN号1549-9618
DOI10.1021/acs.jctc.7b01211
文献子类Article
英文摘要Accelerated Molecular Dynamics (aMD) is a promising enhanced sampling method to explore the conformational space of biomolecules. However, the large statistical noise in reweighting limits its accuracy to recover the original free energy profile. In this work, we propose an Integrated accelerated Molecule Dynamics (IaMD) method by integrating a series of aMD subterms with different acceleration parameters to improve the sampling efficiency and maintain the reweighting accuracy simultaneously. We use Alanine Dipeptide and three fast-folded proteins (Chignolin, Trp-cage, and Villin Headpiece) as the test objects to compare our IaMD method with aMD systematically. These case studies indicate that the statistical noise of IaMD in reweighting for free energy profiles is much smaller than that of aMD at the same level of acceleration and simulation time. To achieve the same accuracy as IaMD, aMD requires 1-3 orders of magnitude longer simulation time, depending on the complexity of the simulated system and the level of acceleration. Our method also outperforms aMD in controlling systematic error caused by the disappearance of the low-energy conformations when high acceleration parameters are used in alVID simulations for fast-folded proteins. Furthermore, the performance comparison between IaMD and the Integrated Tempering Sampling (ITS) in the case of Alanine Dipeptide demonstrates that IaMD possesses a better ability to control the potential energy region of sampling.
WOS关键词REPLICA EXCHANGE APPROACH ; BETA-HAIRPIN PEPTIDE ; THERMODYNAMIC INTEGRATION ; FOLDING PATHWAY ; SIMULATIONS ; PROTEINS ; SYSTEMS ; CONFORMATIONS ; BIOMOLECULES ; TRANSITIONS
WOS研究方向Chemistry ; Physics
语种英语
WOS记录号WOS:000427661400006
出版者AMER CHEMICAL SOC
源URL[http://cas-ir.dicp.ac.cn/handle/321008/168872]  
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1.Chinese Acad Sci, Dalian Inst Chem Phys, State Key Lab Mol React Dynam, Lab Mol Modeling & Design, Dalian 116023, Peoples R China
2.Univ Chinese Acad Sci, Chinese Acad Sci, Beijing 100049, Peoples R China
推荐引用方式
GB/T 7714		 Peng, Xiangda,Zhang, Yuebin,Li, Yan,et al. Integrating Multiple Accelerated Molecular Dynamics To Improve Accuracy of Free Energy Calculations[J]. JOURNAL OF CHEMICAL THEORY AND COMPUTATION,2018,14(3):1216-1227.
APA Peng, Xiangda.,Zhang, Yuebin.,Li, Yan.,Liu, QingLong.,Chu, Huiying.,...&Li, Guohui.(2018).Integrating Multiple Accelerated Molecular Dynamics To Improve Accuracy of Free Energy Calculations.JOURNAL OF CHEMICAL THEORY AND COMPUTATION,14(3),1216-1227.
MLA Peng, Xiangda,et al."Integrating Multiple Accelerated Molecular Dynamics To Improve Accuracy of Free Energy Calculations".JOURNAL OF CHEMICAL THEORY AND COMPUTATION 14.3(2018):1216-1227.

入库方式： OAI收割

来源：大连化学物理研究所

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