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Tutorial 4 — Advanced Path Finding

Tutorial 4: Another reaction path-finding example

This section gives a second example input file set for a typical double-ended reaction path-finding calculation run through CDE.

The calculation set-up is similar to Tutorial 3, but uses a different optimization function (type 4) instead. So, in this example, the target product is a single molecule, whereas the reactants contain a set of different molecular species.

This example can be run in the same way as tutorial 3, and similar input files are output.

The interesting output files are as follows:

  • mcopt.dat: This file contains a running value of the total graph-error function as a function of the number of simulated annealing iterations.

  • input.log: Once the simulated annealing calculation is complete, the log file will contain lots of useful information about the final reaction mechanism (if successful).

  • final_path.xyz: Contains an xyz file with molecular snapshots of the intermediates generated along the final reaction-path.

  • final_path_rx_ZZZ.xyz: Contains an approximation to the reaction-path for reaction-step ZZZ in the final mechanism.

  • adjusted_path_ZZZ.xyz: These adjusted xyz files contain only those molecules which are relevant to the formation of the product of interest.

The xyz files can obviously be plotted in VMD in order to visualize the reaction.