Free Energy Simulations with the AMOEBA Polarizable Force Field and Metadynamics on GPU Platform
文献类型：期刊论文
| 作者 | Zhang, Yuebin; Li, Guohui; Peng, Xiangda; Chu, Huiying |
| 刊名 | JOURNAL OF COMPUTATIONAL CHEMISTRY
 |
| 出版日期 | 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 |
| WOS记录号 | WOS:000370254600009 |
| 出版者 | WILEY-BLACKWELL |
| 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. |
入库方式： OAI收割
来源：大连化学物理研究所
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