First-principles molecular dynamics (FPMD) simulations are highly accurate, but due to their high calculation cost, the computational scale is often limited to hundreds of atoms and few picoseconds under specific temperature and pressure conditions. We present here the guidelines for creating artificial neural network empirical interatomic potential (ANN potential) trained with such a limited FPMD data, which can perform long time scale MD simulations at least under the same conditions. The FPMD data for training are prepared on the basis of the convergence of radial distribution function [g(r)]. While training the ANN using total energy and atomic forces of the FPMD data, the error of pressure is also monitored and minimized. To create further robust potential, we add a small amount of FPMD data to reproduce the interaction between two atoms that are close to each other. ANN potentials for α-AgSe were created as an application example, and it has been confirmed that not only g(r) and mean square displacements but also the specific heat requiring a long time scale simulation matched the FPMD and the experimental values. In addition, the MD simulation using the ANN potential achieved over 10 acceleration over the FPMD one. The guidelines proposed here mitigate the creation difficulty of the ANN potential, and a lot of FPMD data sleeping on the hard disk after the research may be put on the front stage again.
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http://dx.doi.org/10.1063/1.5116420 | DOI Listing |
Inorg Chem
December 2024
State Key Laboratory for Mineral Deposits Research, School of Earth Sciences and Engineering, Nanjing University, Nanjing, Jiangsu 210023, China.
In this study, we employed classical molecular dynamics (CMD) and first-principles molecular dynamics (FPMD) simulations to investigate the speciation of uranyl in carbonate-rich hydrothermal solutions. The association constants (log) of uranyl carbonate complexes were derived from the potential of mean forces (PMFs) obtained from CMD simulations, and the acid constants (ps) of uranyl aqua ions were calculated using the FPMD-based vertical energy gap method. The results showed that uranyl ions could form stable mono- and bi-carbonate complexes at elevated temperatures and that uranyl aqua ions strongly hydrolyzed in neutral solutions at temperatures exceeding 473 K.
View Article and Find Full Text PDFNutrients
August 2023
Department of Orthopedic Surgery, Seoul National University College of Medicine, Boramae Hospital, Seoul 07061, Republic of Korea.
Osteoarthritis is a significant global health problem. Many patients seek more effective alternatives to nonsteroidal anti-inflammatory medicines or commercial supplements to manage joint pain and inflammation. FlexPro MD (FP-MD) combines krill oil, astaxanthin, and lower molecular weight hyaluronic acid to support joint health.
View Article and Find Full Text PDFPlant Dis
March 2023
National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Shandong 271018, China.
Apple replant disease (ARD) caused by the fungal pathogen f. sp. () MR5 brings annual losses to apple production within China.
View Article and Find Full Text PDFMolecules
December 2022
Institut de Physique et Chimie des Matériaux de Strasbourg, Université de Strasbourg, CNRS, F-67034 Strasbourg, France.
First-principles molecular dynamics (FPMD) calculations were performed on liquid GeSe with the aim of inferring the impact of dispersion (van der Waals, vdW) forces on the structural properties. Different expressions for the dispersion forces were employed, allowing us to draw conclusions on their performances in a comparative fashion. These results supersede previous FPMD calculations obtained in smaller systems and shorter time trajectories by providing data of unprecedented accuracy.
View Article and Find Full Text PDFJ Phys Chem Lett
December 2021
Computational Laboratory for Hybrid/Organic Photovoltaics (CLHYO), Istituto CNR di Scienze e Tecnologie Chimiche "Giulio Natta" (CNR-SCITEC), Via Elce di Sotto 8, 06123 Perugia, Italy.
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