title: Reaction analysis and visualization of ReaxFF molecular dynamics simulations.
abstract: 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.
authors: State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China.
authors: Jian
authors: J
authors: Liu
authors: State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China. Electronic address: xxia@ipe.ac.cn.
authors: Xiaoxia
authors: X
authors: Li
authors: State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China. Electronic address: lguo@ipe.ac.cn.
authors: Li
authors: L
authors: Guo
authors: State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China.
authors: Mo
authors: M
authors: Zheng
authors: State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China.
authors: Junyi
authors: J
authors: Han
authors: State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China.
authors: Xiaolong
authors: X
authors: Yuan
authors: State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China.
authors: Fengguang
authors: F
authors: Nie
authors: State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China.
authors: Xiaolong
authors: X
authors: Liu
mesh_terms: D000465:Algorithms; D003196:Computer Graphics; D008956:Models, Chemical; D056004:Molecular Dynamics Simulation; D011789:Quantum Theory; D014584:User-Computer Interface
keywords: Chemical reaction analysis and visualization; Chemical reaction mechanisms; Chemical reaction parsing; Chemical structure processing; Cheminformatics; Large scale simulation; Reaction pathway analysis; ReaxFF molecular dynamics; VARxMD