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A Postprocessing Tool for Efficient Molecular Reaction Path Analysis in Kinetic Simulations
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DOI：10.1021/acs.jcim.5c01229.png)
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Abstract
En 中文
This study presents a Python-based tool for extracting molecular reaction pathways from kinetic simulation trajectory files. Compared to traditional depth first search (DFS) and breadth first search (BFS) algorithms, a more efficient chain analysis algorithm is introduced. The tool utilizes a full-time domain response analysis approach, enabling the identification of reactions across nonadjacent frames, thereby enhancing the comprehensiveness of the analysis. The responses are stored in a directed graph structure, and full integration of parallel computing significantly improves processing efficiency. The tool supports molecular dynamics, ab initio molecular dynamics, and coarse-grained simulations. As an open-source Python project, it offers both portability and wide applicability. The reaction processes in a propyne-ethylene blending system and the cross-linking reaction in an epoxy resin coarse-grained system are demonstrated, highlighting the tool’s potential for analyzing various molecular systems.
Keywords:
molecular reaction pathways
kinetic simulation
chain analysis algorithm
directed graph
parallel computing
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