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Reaction analysis and visualization of ReaxFF molecular dynamics simulations
Alternative TitleJ. Mol. Graph.
Liu, Jian1,2; Li, Xiaoxia1; Guo, Li1; Zheng, Mo1,2; Han, Junyi1,2; Yuan, Xiaolong1; Nie, Fengguang1; Liu, Xiaolong1,2
2014-09-01
Source PublicationJOURNAL OF MOLECULAR GRAPHICS & MODELLING
ISSN1093-3263
Volume53Issue:sepPages:13-22
AbstractReaxFF 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.; 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.
KeywordReaxff Molecular Dynamics Large Scale Simulation Varxmd Chemical Reaction Analysis And Visualization Chemical Reaction Mechanisms Cheminformatics Chemical Reaction Parsing Reaction Pathway Analysis Chemical Structure Processing
SubtypeArticle
WOS HeadingsScience & Technology ; Life Sciences & Biomedicine ; Technology ; Physical Sciences
DOI10.1016/j.jmgm.2014.07.002
URL查看原文
Indexed BySCI
Language英语
WOS KeywordBOND ORDER ASSIGNMENT ; FORCE-FIELD ; COAL PYROLYSIS ; PERCEPTION ; DECOMPOSITION ; INFORMATION ; FRAMEWORK ; KINETICS ; INCHI
WOS Research AreaBiochemistry & Molecular Biology ; Computer Science ; Crystallography ; Mathematical & Computational Biology
WOS SubjectBiochemical Research Methods ; Biochemistry & Molecular Biology ; Computer Science, Interdisciplinary Applications ; Crystallography ; Mathematical & Computational Biology
WOS IDWOS:000343631800002
Citation statistics
Cited Times:30[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.ipe.ac.cn/handle/122111/11681
Collection研究所(批量导入)
Affiliation1.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
Recommended Citation
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.
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