What is REACTER?
It is an extension of classical molecular dynamics (MD) that allows molecules to update their bond connectivity during a running simulation. This new protocol can allow traditional fixed valence MD force fields to approximate reactions in a completely classical setting. It is useful for building initial configurations for complex amorphous materials whose reaction mechanisms are known, or to examine the structure and properties of materials produced using one or more proposed mechanisms.
How does it work?
REACTER requires as input two user-provided molecular templates. These pre- and post-reaction templates are used to carry out a specific reaction. Candidate reactants in a running MD simulation are first identified by interatomic separation, followed by the application of a generalized topology matching algorithm to confirm they match the pre-reaction template. If the reactants meet all other user-specified constraints, this is followed by a topology conversion to match the post-reaction template and a dynamic relaxation to minimize high energy configurations.
Why is it useful?
As compared to traditional fixed valence MD force fields, reactive force fields such as the popular ReaxFF require potential energy expressions that are much more complex and remain difficult to parameterize accurately. They are also more computationally expensive, which dramatically limits the practical size and duration of the simulations that can be performed, relative to those done with fixed valence force fields.
What can it not do?
REACTER is only useful for reactions with known mechanisms or for comparing the effects of two or more different reaction mechanisms. Other methods, such as quantum mechanical modeling, path-integral molecular dynamics, or reactive empirical potentials, are more appropriate for cases in which predicting reactivity or reaction mechanisms is the objective.
How can I use it?
REACTER is currently implemented in LAMMPS as fix bond/react. General questions on its usage can be directed to the LAMMPS forum on matsci.org. For a suggested workflow and other usage tips, visit Tutorials and Documentation. Several example systems (nylon, epoxy, polystyrene) are available with the free LAMMPS software (examples/PACKAGES/reaction). Please direct any additional questions to firstname.lastname@example.org.
Can I contribute?
Please do! REACTER is under active development, and we are interested in hearing about new applications, feature ideas or contributed code.