In Molecular Dynamics (MD), standard force fields inherently lack the capacity for simulating chemical reactions. Among many other methods such as QM/MM, hybrid MD/MC simulations can be used for reactive systems[1]. With such a setup, changes within the molecular system require an adjustment of force field parameters to accurately reflect the current system state.
Here, we present how the open-source framework KIMMDY[2] handles on-the-fly reparametrization after reactions. This parametrization strategy allows for automated consecutive MD simulations of reactive systems within a KIMMDY run.
From a MD engine perspective, the molecule parameters as well as its coordinates need to be adapted to continue simulating from the product state. Addressing this, we’ve designed reaction steps in KIMMDY. To accommodate changes in parameters, the system’s connectivity can be adjusted through bond breaking and forming steps, followed by reparametrization with GRAPPA[3]. Additionally, for adjustments of coordinates, KIMMDY features a "place atom" step, allowing for the repositioning of atoms. This is complemented by a relaxation MD step, which may include slow growth parameter transitions to smoothly integrate parameter changes, ensuring the system reaches its intended state without artifacts. Different reaction scenarios are explored to highlight the expressivity of KIMMDY reaction steps.
Eric Hartmann