Reaction analysis and visualization of ReaxFF molecular dynamics simulations
文献类型：期刊论文
| 作者 | Liu, Jian1,2; Li, Xiaoxia1; Guo, Li1; Zheng, Mo1,2; Han, Junyi1,2; Yuan, Xiaolong1; Nie, Fengguang1; Liu, Xiaolong1,2 |
| 刊名 | JOURNAL OF MOLECULAR GRAPHICS & MODELLING
 |
| 出版日期 | 2014-09-01 |
| 卷号 | 53期号:sep页码:13-22 |
| 关键词 | ReaxFF molecular dynamics Large scale simulation VARxMD Chemical reaction analysis and visualization Chemical reaction mechanisms Cheminformatics Chemical reaction parsing Reaction pathway analysis Chemical structure processing |
| ISSN号 | 1093-3263 |
| 其他题名 | J. Mol. Graph. |
| 中文摘要 | ReaxFF MD (Reactive Force Field Molecular Dynamics) is a promising method for investigating complex chemical reactions in relatively larger scale molecular systems. The existing analysis tools for ReaxFF MD lack the capability of capturing chemical reactions directly by analyzing the simulation trajectory, which is critical in exploring reaction mechanisms. This paper presents the algorithms, implementation strategies, features, and applications of VARxMD, a tool for Visualization and Analysis of Reactive Molecular Dynamics. VARxMD is dedicated to detailed chemical reaction analysis and visualization from the trajectories obtained in ReaxFF MD simulations. The interrelationships among the atoms, bonds, fragments, species and reactions are analyzed directly from the three-dimensional (3D) coordinates and bond orders of the atoms in a trajectory, which are accomplished by determination of atomic connectivity for recognizing connected molecular fragments, perception of bond types in the connected fragments for molecules or radicals, indexing of all these molecules or radicals (chemical species) based on their 3D coordinates and recognition of bond breaking or forming in the chemical species for reactions. Consequently, detailed chemical reactions taking place between two sampled frames can be generated automatically. VARxMD is the first tool specialized for reaction analysis and visualization in ReaxFF MD simulations. Applications of VARxMD in ReaxFF MD simulations of coal and HDPE (high-density polyethylene) pyrolysis show that VARxMD provides the capabilities in exploring the reaction mechanism in large systems with complex chemical reactions involved that are difficult to access manually. (C) 2014 Elsevier Inc. All rights reserved. |
| 英文摘要 | ReaxFF MD (Reactive Force Field Molecular Dynamics) is a promising method for investigating complex chemical reactions in relatively larger scale molecular systems. The existing analysis tools for ReaxFF MD lack the capability of capturing chemical reactions directly by analyzing the simulation trajectory, which is critical in exploring reaction mechanisms. This paper presents the algorithms, implementation strategies, features, and applications of VARxMD, a tool for Visualization and Analysis of Reactive Molecular Dynamics. VARxMD is dedicated to detailed chemical reaction analysis and visualization from the trajectories obtained in ReaxFF MD simulations. The interrelationships among the atoms, bonds, fragments, species and reactions are analyzed directly from the three-dimensional (3D) coordinates and bond orders of the atoms in a trajectory, which are accomplished by determination of atomic connectivity for recognizing connected molecular fragments, perception of bond types in the connected fragments for molecules or radicals, indexing of all these molecules or radicals (chemical species) based on their 3D coordinates and recognition of bond breaking or forming in the chemical species for reactions. Consequently, detailed chemical reactions taking place between two sampled frames can be generated automatically. VARxMD is the first tool specialized for reaction analysis and visualization in ReaxFF MD simulations. Applications of VARxMD in ReaxFF MD simulations of coal and HDPE (high-density polyethylene) pyrolysis show that VARxMD provides the capabilities in exploring the reaction mechanism in large systems with complex chemical reactions involved that are difficult to access manually. (C) 2014 Elsevier Inc. All rights reserved. |
| WOS标题词 | Science & Technology ; Life Sciences & Biomedicine ; Technology ; Physical Sciences |
| 类目[WOS] | Biochemical Research Methods ; Biochemistry & Molecular Biology ; Computer Science, Interdisciplinary Applications ; Crystallography ; Mathematical & Computational Biology |
| 研究领域[WOS] | Biochemistry & Molecular Biology ; Computer Science ; Crystallography ; Mathematical & Computational Biology |
| 关键词[WOS] | BOND ORDER ASSIGNMENT ; FORCE-FIELD ; COAL PYROLYSIS ; PERCEPTION ; DECOMPOSITION ; INFORMATION ; FRAMEWORK ; KINETICS ; INCHI |
| 收录类别 | SCI |
| 原文出处 | |
| 语种 | 英语 |
| WOS记录号 | WOS:000343631800002 |
| 公开日期 | 2014-12-01 |
| 源URL | [http://ir.ipe.ac.cn/handle/122111/11681]  |
| 专题 | 过程工程研究所_研究所（批量导入） |
| 作者单位 | 1.Chinese Acad Sci, Inst Proc Engn, State Key Lab Multiphase Complex Syst, Beijing 100190, Peoples R China 2.Univ Chinese Acad Sci, Beijing 100049, Peoples R China |
| 推荐引用方式 GB/T 7714 | Liu, Jian,Li, Xiaoxia,Guo, Li,et al. Reaction analysis and visualization of ReaxFF molecular dynamics simulations[J]. JOURNAL OF MOLECULAR GRAPHICS & MODELLING,2014,53(sep):13-22. |
| APA | Liu, Jian.,Li, Xiaoxia.,Guo, Li.,Zheng, Mo.,Han, Junyi.,...&Liu, Xiaolong.(2014).Reaction analysis and visualization of ReaxFF molecular dynamics simulations.JOURNAL OF MOLECULAR GRAPHICS & MODELLING,53(sep),13-22. |
| MLA | Liu, Jian,et al."Reaction analysis and visualization of ReaxFF molecular dynamics simulations".JOURNAL OF MOLECULAR GRAPHICS & MODELLING 53.sep(2014):13-22. |
入库方式： OAI收割
来源：过程工程研究所
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