Reaction Analysis for Reactive Molecular Dynamics
Xiaoxia Li1,2* Mo Zheng1,2, Chunxing Ren1, Li
Guo1,2
1 State Key Laboratory of Multiphase Complex Systems, Institute of Process
Engineering, Chinese Academy of Sciences, Beijing 100190；
2 School of Chemical Engineering, University of Chinese Academy of Sciences,
Beijing 100049
ABSTRACT: The reactive molecular
dynamics using ReaxFF force field (ReaxFF MD) is an atomic level simulation
method for continuously describing reaction event evolution of a molecular
system. With no requirement for priori knowledge of reaction pathways and much
reduced computational cost than QM based method for relatively larger molecular
models, though maybe with a loss of accuracy, ReaxFF MD has been found its
unique advantage in investigating reaction mechanism for pyrolysis and
oxidation of carbon based fuels, energetic materials and hydrocarbon fuels.
However, the reaction analysis for pyrolysis and oxidation simulation is beyond
of the capability of available tools. This talk overview the VARxMD code for
reaction analysis and visualization of ReaxFF MD simulations developed in the
authors group. The functions of VARxMD were developed and extended on the basis
of its unique capability for reaction site analysis and visualization. Full
reaction list can be generated automatically from the trajectory and bond order
files. For reaction pathway analysis, reaction categorization can be performed
based on chemical structure searching of reactive species and reaction sites.
Reaction network for specified reactants and products can be generated and
visualized. Reaction tracking can be performed in a picked 3D zone of a
simulation cell. VARxMD is a necessity for large scale ReaxFF MD applications
in understanding the complex reaction mechanism in pyrolysis and oxidation of
organic systems.
Keywords: Reactive
molecular dynamics; ReaxFF; reaction analysis; cheminformatics.
Xiaoxia Li, professor of Institute of Process Engineering, Chinese Academy of Sciences. Have been working on chemical databases, chemistry search engines, and large scale ReaxFF molecular dynamics. The recent methodology development of large scale ReaxFF MD have been applied to challenging problems for revealing mechanism of complex pyrolysis and combustion systems, including polymers, coal, biomass, CL-20 cocrystals, as well as bio-oil and hydrocarbon fuels.