Fully automatic reaction detection for complex systems
Molecular dynamics (MD) simulations are a common way to simulate the time evolution of larger chemical systems. Because MD is often based on classical mechanics, systems can comprise thousands of interacting atoms, making it possible to study a variety of physical and chemical phenomena.
When simulating a reactive system – where chemical bonds between atoms can change over time – it is not uncommon to observe a very large number of reactions. For large or complex simulations, the many reactive events make it challenging to derive meaningful information from the trajectory. ChemTraYzer2 (CT2) is a tool designed to help with this problem. CT2 reads each frame of a reactive MD trajectory, keeps track of all reactions that occur, and summarizes all of this information into several useful quantities:
- A list of all encountered species (reactants, products, intermediates)
- A list of unique reactions
- Reaction rate constants for all reactions
- Net fluxes of each species encountered in the simulation
- Other kinetic and population measures
