GaTewAY : Graph theory-based software for automatic analysis of molecular conformers generated over time

GaTewAY is a post-processing tool for molecular dynamics (MD) simulation databased on graph theoretical techniques. The main idea is to construct 2D graphs from the 3D structures. Then, GaTewAY identifies the conformations over time based on the dynamics of bonds and the isomorphism test. The use of graph theory methods/tools does not only provide a direct and fast methodology to identify conformers, but also allows following in time the interconversion reactions between the different conformers as shown by graphs of transitions. In this paper, we describe the methodology used to develop GaTeWAY. Then, we describe the code with its different modules. We present the inputs of GaTeWAY, the threshold values, the usage of the code and the main outputs. Our software has been tested and validated on DFT-MD and QM-MM trajectories of gas phase molecules and clusters. We will, in particular, illustrate results for peptides to have an idea about the outputs. The algorithm's transferability is further demonstrated on a more complex air/liquid water interface. We designed our algorithm so that it can be extended and consider any types of bonds/interactions and parameters; hence, GaTeWAY can be applied to any molecular system. Ongoing work aims to analyze reaction networks in clusters for catalysis. The results are promising. Another manuscript has just been submitted, which illustrates the performance of GateWAY for these systems.