The geometry optimization of a water molecule with a novel type of energy function called FFLUX is presented, which bypasses the traditional bonded potentials. Instead, topologically-partitioned atomic energies are trained by the machine learning method kriging to predict their IQA atomic energies for a previously unseen molecular geometry. Proof-of-concept that FFLUX’s architecture is suitable for geometry optimization is rigorously demonstrated. It is found that accurate kriging models can optimize 2000 distorted geometries to within 0.28 kJ mol−1 of the corresponding ab initio energy, and 50% of those to within 0.05 kJ mol−1. Kriging models are robust enough to optimize the molecular geometry to sub-noise accuracy, when two thirds of the geometric inputs are outside the training range of that model. Finally, the individual components of the potential energy are analyzed, and chemical intuition is reflected in the independent behavior of the three energy terms (intra-atomic), (electrostatic) and (exchange), in contrast to standard force fields.
Present computing power enables novel ways of modeling polarization. Here we show that the machine learning method kriging accurately captures the way the electron density of a topological atom responds to a change in the positions of the surrounding atoms. The success of this method is demonstrated on the four aromatic amino acids histidine, phenylalanine, tryptophan, and tyrosine. A new technique of varying training set sizes to vastly reduce training times while maintaining accuracy is described and applied to each amino acid. Each amino acid has its geometry distorted via normal modes of vibration over all local energy minima in the Ramachandran map. These geometries are then used to train the kriging models. Total electrostatic energies predicted by the kriging models for previously unseen geometries are compared to the true energies, yielding mean absolute errors of 2.9, 5.1, 4.2, and 2.8 kJ mol(-1) for histidine, phenylalanine, tryptophan, and tyrosine, respectively.
The machine learning method kriging is an attractive tool to construct next-generation force fields. Kriging can accurately predict atomistic properties, which involves optimization of the so-called concentrated log-likelihood function (i.e., fitness function). The difficulty of this optimization problem quickly escalates in response to an increase in either the number of dimensions of the system considered or the size of the training set. In this article, we demonstrate and compare the use of two search algorithms, namely, particle swarm optimization (PSO) and differential evolution (DE), to rapidly obtain the maximum of this fitness function. The ability of these two algorithms to find a stationary point is assessed by using the first derivative of the fitness function. Finally, the converged position obtained by PSO and DE is refined through the limited-memory Broyden-Fletcher-Goldfarb-Shanno bounded (L-BFGS-B) algorithm, which belongs to the class of quasi-Newton algorithms. We show that both PSO and DE are able to come close to the stationary point, even in high-dimensional problems. They do so in a reasonable amount of time, compared to that with the Newton and quasi-Newton algorithms, regardless of the starting position in the search space of kriging hyperparameters. The refinement through L-BFGS-B is able to give the position of the maximum with whichever precision is desired.
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