Neural network potentials (NNPs) are gaining much attention as they enable fast molecular dynamics (MD) simulations for a wide range of systems while maintaining the accuracy of density functional theory calculations. Since NNP is constructed by machine learning on training data, its prediction uncertainty increases drastically as atomic environments deviate from training points. Therefore, it is essential to monitor the uncertainty level during MD simulations to judge the soundness of the results. In this work, we propose an uncertainty estimator based on the replica ensemble in which NNPs are trained over atomic energies of a reference NNP that drives MD simulations. The replica ensemble is trained quickly, and its standard deviation provides atomic-resolution uncertainties. We apply this method to a highly reactive silicidation process of Si(001) overlaid with Ni thin films and confirm that the replica ensemble can spatially and temporally trace simulation errors at atomic resolution, which in turn guides the augmentation of the training set. The refined NNP completes a 3.6 ns simulation without any noticeable problems. By suggesting an efficient and atomic-resolution uncertainty indicator, this work will contribute to achieving reliable MD simulations by NNPs.
Download full-text PDF |
Source |
---|---|
http://dx.doi.org/10.1021/acs.jpclett.0c01614 | DOI Listing |
J Chem Inf Model
January 2025
Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States.
The separation and structural identification of glycans are of great bioanalytical importance. To obtain a good understanding of the structural flexibility of glycans, replica exchange molecular dynamics (REMD) simulations were used based on AMBER force field calculations to create ensembles of glycan structures. Nonpolar surface area (NPSA) calculations based on continuum solvation (CS) models (Dhakal, R.
View Article and Find Full Text PDFPolym Chem
August 2024
Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.
While the conformational ensembles of disordered peptides and peptidomimetics are complex and challenging to characterize, they are a critical component in the paradigm connecting macromolecule sequence, structure, and function. In molecules that do not adopt a single predominant conformation, the conformational ensemble contains rich structural information that, if accessible, can provide a fundamental understanding related to desirable functions such as cell penetration of a therapeutic or the generation of tunable enzyme-mimetic architecture. To address the fundamental challenge of describing broad conformational ensembles, we developed a model system of peptidomimetics comprised of polar glycine and hydrophobic -butylglycine to characterize using a suite of analytical techniques.
View Article and Find Full Text PDFJ Chem Theory Comput
January 2025
Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States.
Relative free energy (RFE) calculations are now widely used in academia and the industry, but their accuracy is often limited by poor sampling of the complexes' conformational ensemble. To help address conformational sampling problems when simulating many relative binding free energies, we developed a novel method termed multiple topology replica exchange of expanded ensembles (MT-REXEE). This method enables parallel expanded ensemble calculations, facilitating iterative RFE computations while allowing conformational exchange between parallel transformations.
View Article and Find Full Text PDFMicrolife
December 2024
Department of Molecular Evolution, Centro de Astrobiología (CAB), CSIC-INTA, Torrejón de Ardoz,28864 Madrid, Spain.
Evolutionary processes acting on populations of organized molecules preceded the origin of living organisms. These prebiotic entities were independently and repeatedly produced [i.e.
View Article and Find Full Text PDFInt J Mol Sci
November 2024
Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.
Src kinase is one of the key regulators of cellular metabolism and is dysregulated in numerous diseases, including cancer, neurodegenerative diseases, and particularly Alzheimer's disease. Despite its therapeutic importance, its full-length structure has never been obtained before, as it contains an intrinsically disordered regulatory region, SH4UD. The SH4UD region is crucial for Src activation, functional dimerization, and regulation by other kinases.
View Article and Find Full Text PDFEnter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!