RESUMEN
The reactive force field (ReaxFF) model bridges the gap between traditional classical models and quantum mechanical (QM) models by incorporating dynamic bonding and polarizability. To achieve realistic simulations using ReaxFF, model parameters must be optimized against high fidelity training data which typically come from QM calculations. Existing parameter optimization methods for ReaxFF consist of black box techniques using genetic algorithms or Monte Carlo methods. Due to the stochastic behavior of these methods, the optimization process oftentimes requires millions of error evaluations for complex parameter fitting tasks, thereby significantly hampering the rapid development of high quality parameter sets. Rapid optimization of the parameters is essential for developing and refining Reax force fields because producing a force field which exhibits empirical accuracy in terms of dynamics typically requires multiple refinements to the training data as well as to the parameters under optimization. In this work, we present JAX-ReaxFF, a novel software tool that leverages modern machine learning infrastructure to enable fast optimization of ReaxFF parameters. By calculating gradients of the loss function using the JAX library, JAX-ReaxFF utilizes highly effective local optimization methods that are initiated from multiple guesses in the high dimensional optimization space to obtain high quality results. Leveraging the architectural portability of the JAX framework, JAX-ReaxFF can execute efficiently on multicore CPUs, graphics processing units (GPUs), or even tensor processing units (TPUs). As a result of using the gradient information and modern hardware accelerators, we are able to decrease ReaxFF parameter optimization time from days to mere minutes. Furthermore, the JAX-ReaxFF framework can also serve as a sandbox environment for domain scientists to explore customizing the ReaxFF functional form for more accurate modeling.
RESUMEN
A novel locally polarizable multisite model based on the original cation dummy atom (CDA) model is described for molecular dynamics simulations of ions in condensed phases. Polarization effects are introduced by the electronegativity equalization model (EEM) method where charges on the metal ion and its dummy atoms can fluctuate to respond to the environment. This model includes explicit polarization and ion-induced interactions and can be coupled with nonpolarizable or polarizable water models, making it more transferable to simpler force fields. This approach allows us to enhance the original fixed charge CDA model where the charge distribution cannot adapt to the local solvent structure. To illustrate the new CDApol model, we examined properties of the Zn2+, Al3+, and Zr4+ ions in aqueous solution. The polarizable model and Lennard-Jones parameters were refined for octahedrally coordinated Zn2+, Al3+, and Zr4+ CDAs to reproduce thermodynamic and geometrical properties. Using this locally polarizable model, we were able to obtain the experimental hydration free energy, ion-oxygen distance, and coordination number coupled with the standard 12-6 Lennard-Jones model. This model can be used in myriad additional applications where local polarization and charge transfer is important.
RESUMEN
Combined quantum mechanical/molecular mechanical (QM/MM) models using semiempirical and ab initio methods have been extensively reported on over the past few decades. These methods have been shown to be capable of providing unique insights into a range of problems, but they are still limited to relatively short time scales, especially QM/MM models using ab initio methods. An intermediate approach between a QM based model and classical mechanics could help fill this time-scale gap and facilitate the study of a range of interesting problems. Reactive force fields represent the intermediate approach explored in this paper. A widely used reactive model is ReaxFF, which has largely been applied to materials science problems and is generally used as a stand-alone (i.e., the full system is modeled using ReaxFF). We report a hybrid ReaxFF/AMBER molecular dynamics (MD) tool, which introduces ReaxFF capabilities to capture bond breaking and formation within the AMBER MD software package. This tool enables us to study local reactive events in large systems at a fraction of the computational costs of QM/MM models. We describe the implementation of ReaxFF/AMBER, validate this implementation using a benzene molecule solvated in water, and compare its performance against a range of similar approaches. To illustrate the predictive capabilities of ReaxFF/AMBER, we carried out a Claisen rearrangement study in aqueous solution. In a first for ReaxFF, we were able to use AMBER's potential of mean force (PMF) capabilities to perform a PMF study on this organic reaction. The ability to capture local reaction events in large systems using combined ReaxFF/AMBER opens up a range of problems that can be tackled using this model to address both chemical and biological processes.