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Register a new userSchrodinger-ANI: An Eight-Element Neural Network Interaction Potential with Greatly Expanded Coverage of Druglike Chemical Space
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We have developed a neural network potential energy function for use in drug discovery, with chemical element support extended from 41% to 94% of druglike molecules based on ChEMBL. We expand on the work of Smith et al., with their highly accurate network for the elements H, C, N, O, creating a network for H, C, N, O, S, F, Cl, P. We focus particularly on the calculation of relative conformer energies, for which we show that our new potential energy function has an RMSE of 0.70 kcal/mol for prospective druglike molecule conformers, substantially better than the previous state of the art. The speed and accuracy of this model could greatly accelerate the parameterization of protein-ligand binding free energy calculations for novel druglike molecules.
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One hidden yet important issue for developing neural network potentials (NNPs) is the choice of training algorithm. Here we compare the performance of two popular training algorithms, the adaptive moment estimation algorithm (Adam) and the extended Kalman filter algorithm (EKF), using the Behler-Parrinello neural network (BPNN) and two publicly accessible datasets of liquid water. It is found that NNPs trained with EKF are more transferable and less sensitive to the value of the learning rate, as compared to Adam. In both cases, error metrics of the test set do not always serve as a good indicator for the actual performance of NNPs. Instead, we show that their performance correlates well with a Fisher information based similarity measure.
Deep learning techniques have opened a new venue for electronic structure theory in recent years. In contrast to traditional methods, deep neural networks provide much more expressive and flexible wave function ansatz, resulting in better accuracy and time scaling behavior. In order to study larger systems while retaining sufficient accuracy, we integrate a powerful neural-network based model (FermiNet) with the effective core potential method, which helps to reduce the complexity of the problem by replacing inner core electrons with additional semi-local potential terms in Hamiltonian. In this work, we calculate the ground state energy of 3d transition metal atoms and their monoxide which are quite challenging for original FermiNet work, and the results are in good consistency with both experimental data and other state-of-the-art computational methods. Our development is an important step for a broader application of deep learning in the electronic structure calculation of molecules and materials.
Most of current neural network models in quantum chemistry (QC) exclude the molecular symmetry, separate the well-correlated real space (R space), and momenta space (K space) into two individuals, which lack the essential physics in molecular chemistry. In this work, by endorsing the molecular symmetry and elementals of group theory, we propose a comprehensive method to apply symmetry in the graph neural network (SY-GNN), which extends the property-predicting coverage to all the orbital symmetry for both ground and excited states. SY-GNN shows excellent performance in predicting both the absolute and relative of R and K spaces quantities. Besides the numerical properties, SY-GNN also can predict the orbitals distributions in real space, providing the active regions of chemical reactions. We believe the symmetry endorsed deep learning scheme covers the significant physics inside and is essential for the application of neural networks in QC and many other research fields in the future.
Artificial neural network modeling does not need to consider the mechanism. It can map the implicit relationship between input and output and predict the performance of the system well. At the same time, it has the advantages of self-learning ability and high fault tolerance. The gas-liquid two phases in the rectification tower conduct interphase heat and mass transfer through countercurrent contact. The functional relationship between the product concentration at the top and bottom of the tower and the process parameters is extremely complex. The functional relationship can be accurately controlled by artificial neural network algorithms. The key components of the propylene distillation tower are the propane concentration at the top of the tower and the propylene concentration at the bottom of the tower. Accurate measurement of them plays a key role in increasing propylene yield in ethylene production enterprises. This article mainly introduces the neural network model and its application in the propylene distillation tower.
The numerical computation of chemical potential in dense, non-homogeneous fluids is a key problem in the study of confined fluids thermodynamics. To this day several methods have been proposed, however there is still need for a robust technique, capable of obtaining accurate estimates at large average densities. A widely established technique is the Widom insertion method, that computes the chemical potential by sampling the energy of insertion of a test particle. Non-homogeneity is accounted for by assigning a density dependent weight to the insertion points. However, in dense systems, the poor sampling of the insertion energy is a source of inefficiency, hampering a reliable convergence. We have recently presented a new technique for the chemical potential calculation in homogeneous fluids. This novel method enhances the sampling of the insertion energy via Well-Tempered Metadynamics, reaching accurate estimates at very large densities. In this paper we extend the technique to the case of non-homogeneous fluids. The method is successfully tested on a confined Lennard-Jones fluid. In particular we show that, thanks to the improved sampling, our technique does not suffer from a systematic error that affects the classic Widom method for non-homogeneous fluids, providing a precise and accurate result.
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