PMID- 25064439
OWN - NLM
STAT- MEDLINE
DCOM- 20150615
LR  - 20170924
IS  - 1873-4243 (Electronic)
IS  - 1093-3263 (Linking)
VI  - 53
DP  - 2014 Sep
TI  - Reaction analysis and visualization of ReaxFF molecular dynamics simulations.
PG  - 13-22
LID - S1093-3263(14)00110-7 [pii]
LID - 10.1016/j.jmgm.2014.07.002 [doi]
AB  - 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.
CI  - Copyright (c) 2014 Elsevier Inc. All rights reserved.
FAU - Liu, Jian
AU  - Liu J
AD  - 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.
FAU - Li, Xiaoxia
AU  - Li X
AD  - 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.
FAU - Guo, Li
AU  - Guo L
AD  - 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.
FAU - Zheng, Mo
AU  - Zheng M
AD  - 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.
FAU - Han, Junyi
AU  - Han J
AD  - 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.
FAU - Yuan, Xiaolong
AU  - Yuan X
AD  - State Key Laboratory of Multiphase Complex Systems, Institute of Process 
      Engineering, Chinese Academy of Sciences, Beijing 100190, PR China.
FAU - Nie, Fengguang
AU  - Nie F
AD  - State Key Laboratory of Multiphase Complex Systems, Institute of Process 
      Engineering, Chinese Academy of Sciences, Beijing 100190, PR China.
FAU - Liu, Xiaolong
AU  - Liu X
AD  - 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.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20140711
PL  - United States
TA  - J Mol Graph Model
JT  - Journal of molecular graphics & modelling
JID - 9716237
SB  - IM
MH  - Algorithms
MH  - Computer Graphics
MH  - Models, Chemical
MH  - *Molecular Dynamics Simulation
MH  - Quantum Theory
MH  - *User-Computer Interface
OTO - NOTNLM
OT  - Chemical reaction analysis and visualization
OT  - Chemical reaction mechanisms
OT  - Chemical reaction parsing
OT  - Chemical structure processing
OT  - Cheminformatics
OT  - Large scale simulation
OT  - Reaction pathway analysis
OT  - ReaxFF molecular dynamics
OT  - VARxMD
EDAT- 2014/07/30 06:00
MHDA- 2015/06/16 06:00
CRDT- 2014/07/28 06:00
PHST- 2014/03/02 00:00 [received]
PHST- 2014/07/01 00:00 [revised]
PHST- 2014/07/03 00:00 [accepted]
PHST- 2014/07/28 06:00 [entrez]
PHST- 2014/07/30 06:00 [pubmed]
PHST- 2015/06/16 06:00 [medline]
AID - S1093-3263(14)00110-7 [pii]
AID - 10.1016/j.jmgm.2014.07.002 [doi]
PST - ppublish
SO  - J Mol Graph Model. 2014 Sep;53:13-22. doi: 10.1016/j.jmgm.2014.07.002. Epub 2014 
      Jul 11.