ArticleChemical science2019
Towards large scale hybrid QM/MM dynamics of complex systems with advanced point dipole polarizable embeddings.
Article in Chemical science, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
20 citing papers in PubMed.
- Effective Quantum Theory of EXAFS in a Dissipative Liquid-Phase Medium.The journal of physical chemistry. B · 2026Article
- Method and Implementation of Projected Hybrid Orbitals for Treating Multiple Covalent Bonds in Combined QM/MM Calculations.Journal of chemical theory and computation · 2024Article
- A Quasi Time-Reversible Scheme Based on Density Matrix Extrapolation on the Grassmann Manifold for Born-Oppenheimer Molecular Dynamics.The journal of physical chemistry letters · 2023Article
- Scalable hybrid deep neural networks/polarizable potentials biomolecular simulations including long-range effects.Chemical science · 2023Article
- Fast Method for Excited-State Dynamics in Complex Systems and Its Application to the Photoactivation of a Blue Light Using Flavin Photoreceptor.The journal of physical chemistry letters · 2023Article
- Newton-X Platform: New Software Developments for Surface Hopping and Nuclear Ensembles.Journal of chemical theory and computation · 2022Article
- Trajectory Surface Hopping for a Polarizable Embedding QM/MM Formulation.The journal of physical chemistry. A · 2022Article
- Factors That Determine the Variation of Equilibrium and Kinetic Properties of QM/MM Enzyme Simulations: QM Region, Conformation, and Boundary Condition.Journal of chemical theory and computation · 2022Article
- Computationally driven discovery of SARS-CoV-2 MChemical science · 2022Article
- Grassmann Extrapolation of Density Matrices for Born-Oppenheimer Molecular Dynamics.Journal of chemical theory and computation · 2021Article
- Ultrafast Transient Infrared Spectroscopy of Photoreceptors with Polarizable QM/MM Dynamics.The journal of physical chemistry. B · 2021Article
- Combining Evolutionary Conservation and Quantum Topological Analyses To Determine Quantum Mechanics Subsystems for Biomolecular Quantum Mechanics/Molecular Mechanics Simulations.Journal of chemical theory and computation · 2021Article
- Atomistic Polarizable Embeddings: Energy, Dynamics, Spectroscopy, and Reactivity.Accounts of chemical research · 2021Article
- Biomolecular Modeling and Simulation: A Prospering Multidisciplinary Field.Annual review of biophysics · 2021Article
- High-resolution mining of the SARS-CoV-2 main protease conformational space: supercomputer-driven unsupervised adaptive sampling.Chemical science · 2021Article
- Biomolecular QM/MM Simulations: What Are Some of the "Burning Issues"?The journal of physical chemistry. B · 2021Article
- A simplified charge projection scheme for long-range electrostatics in ab initio QM/MM calculations.The Journal of chemical physics · 2021Article
- A Many-Body, Fully Polarizable Approach to QM/MM Simulations.Journal of chemical theory and computation · 2020Article
- Accurate Biomolecular Simulations Account for Electronic Polarization.Frontiers in molecular biosciences · 2019Article
- Development and application of quantum mechanics/molecular mechanics methods with advanced polarizable potentials.Wiley interdisciplinary reviews. Computational molecular scienceArticle
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
Abstract
In this work, we present a general route to hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) Molecular Dynamics for complex systems using a polarizable embedding. We extend the capabilities of our hybrid framework, combining the Gaussian and Tinker/Tinker-HP packages in the context of the AMOEBA polarizable force field to treat large (bio)systems where the QM and the MM subsystems are covalently bound, adopting pseudopotentials at the boundaries between the two regions. We discuss in detail the implementation and demonstrate the global energy conservation of our QM/MM Born-Oppenheimer molecular dynamics approach using Density Functional Theory. Finally, the approach is assessed on the electronic absorption properties of a 16 500 atom complex encompassing an organic dye embedded in a DNA matrix in solution, extending the hybrid method to a time-dependent Density Functional Theory approach. The results obtained comparing different partitions between the quantum and the classical subsystems also suggest that large QM portions are not necessary if accurate polarizable force fields are used in a variational formulation of the embedding, properly including the QM/MM mutual polarization.
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.