Cargando…

Towards large scale hybrid QM/MM dynamics of complex systems with advanced point dipole polarizable embeddings

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...

Descripción completa

Detalles Bibliográficos
Autores principales:	Loco, Daniele, Lagardère, Louis, Cisneros, Gérardo A., Scalmani, Giovanni, Frisch, Michael, Lipparini, Filippo, Mennucci, Benedetta, Piquemal, Jean-Philip
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Royal Society of Chemistry 2019
Materias:	Chemistry
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6677116/ https://www.ncbi.nlm.nih.gov/pubmed/31588288 http://dx.doi.org/10.1039/c9sc01745c

Ejemplares similares

Trajectory Surface Hopping for a Polarizable Embedding QM/MM Formulation
por: Bondanza, Mattia, et al.
Publicado: (2022)

Ultrafast Transient Infrared Spectroscopy of Photoreceptors with Polarizable QM/MM Dynamics
por: Macaluso, Veronica, et al.
Publicado: (2021)

Atomistic Polarizable Embeddings: Energy, Dynamics, Spectroscopy, and Reactivity
por: Loco, Daniele, et al.
Publicado: (2021)

Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields
por: Lagardère, Louis, et al.
Publicado: (2017)

Energy, Structures, and Response Properties with a Fully Coupled QM/AMOEBA/ddCOSMO Implementation
por: Nottoli, Michele, et al.
Publicado: (2021)

A QM/MM Derived Polarizable Water Model for Molecular Simulation
por: Visscher, Koen M., et al.
Publicado: (2018)

Polarizable ab initio QM/MM Study of the Reaction Mechanism of N-tert-Butyloxycarbonylation of Aniline in [EMIm][BF(4)]
por: Vázquez-Montelongo, Erik Antonio, et al.
Publicado: (2018)

Simulating Absorption Spectra of Flavonoids in Aqueous Solution: A Polarizable QM/MM Study
por: Skoko, Sulejman, et al.
Publicado: (2020)

Quantum mechanical static dipole polarizabilities in the QM7b and AlphaML showcase databases
por: Yang, Yang, et al.
Publicado: (2019)

Tinker-HP: Accelerating Molecular Dynamics Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields Using GPUs and Multi-GPU Systems
por: Adjoua, Olivier, et al.
Publicado: (2021)

Interfacing the Core-Shell or the Drude Polarizable Force Field With Car–Parrinello Molecular Dynamics for QM/MM Simulations
por: Sahoo, Sudhir K., et al.
Publicado: (2018)

Electronic absorption spectra of pyridine and nicotine in aqueous solution with a combined molecular dynamics and polarizable QM/MM approach
por: Pagliai, Marco, et al.
Publicado: (2016)

Two-Photon Absorption Cross-Sections in Fluorescent Proteins Containing Non-canonical Chromophores Using Polarizable QM/MM
por: Rossano-Tapia, Maria, et al.
Publicado: (2020)

Probing Origin of Binding Difference of inhibitors to MDM2 and MDMX by Polarizable Molecular Dynamics Simulation and QM/MM-GBSA Calculation
por: Chen, Jianzhong, et al.
Publicado: (2015)

Scalable hybrid deep neural networks/polarizable potentials biomolecular simulations including long-range effects
por: Jaffrelot Inizan, Théo, et al.
Publicado: (2023)

Force-field-enhanced neural network interactions: from local equivariant embedding to atom-in-molecule properties and long-range effects
por: Plé, Thomas, et al.
Publicado: (2023)

Dipole polarizability of neutron-rich nuclei
por: Canto, L F, et al.
Publicado: (1995)

Exploring the Dependence of QM/MM Calculations of Enzyme Catalysis on the Size of the QM Region
por: Jindal, Garima, et al.
Publicado: (2016)

Efficient determination of accurate atomic polarizabilities for polarizeable embedding calculations
por: Schröder, Heiner, et al.
Publicado: (2016)

Review on the QM/MM Methodologies and Their Application to Metalloproteins
por: Tzeliou, Christina Eleftheria, et al.
Publicado: (2022)

QM Cluster or QM/MM in Computational Enzymology: The Test Case of LigW-Decarboxylase
por: Prejanò, Mario, et al.
Publicado: (2018)

Comparative Computational Approach To Study Enzyme Reactions Using QM and QM-MM Methods
por: Yildiz, Ibrahim, et al.
Publicado: (2018)

Dipole Coulomb polarizability in the scattering of halo nuclei
por: Andrés, M V, et al.
Publicado: (1997)

Variation of the electronic dipole polarizability on the reaction path
por: Jędrzejewski, Mateusz, et al.
Publicado: (2013)

How Large Should the QM Region Be in QM/MM Calculations? The Case of Catechol O-Methyltransferase
por: Kulik, Heather J., et al.
Publicado: (2016)

Effect of the QM Size, Basis Set, and Polarization on QM/MM Interaction Energy Decomposition Analysis
por: Pérez-Barcia, Álvaro, et al.
Publicado: (2023)

Fast Method for Excited-State Dynamics in Complex Systems and Its Application to the Photoactivation of a Blue Light Using Flavin Photoreceptor
por: Mazzeo, Patrizia, et al.
Publicado: (2023)

QM/MM study of the reaction mechanism of sulfite oxidase
por: Caldararu, Octav, et al.
Publicado: (2018)

On the Difference Between Additive and Subtractive QM/MM Calculations
por: Cao, Lili, et al.
Publicado: (2018)

QM/MM Calculations with deMon2k
por: Salahub, Dennis R., et al.
Publicado: (2015)

Mechanisms of Proteolytic Enzymes and Their Inhibition in QM/MM Studies
por: Elsässer, Brigitta, et al.
Publicado: (2021)

Do Better Quality Embedding Potentials Accelerate the Convergence of QM/MM Models? The Case of Solvated Acid Clusters
por: Ho, Junming, et al.
Publicado: (2018)

Alternative Pathway for the Reaction Catalyzed by DNA Dealkylase AlkB from Ab Initio QM/MM Calculations
por: Fang, Dong, et al.
Publicado: (2014)

Exploring the dipole polarizability of $^{11}$Li at REX-ISOLDE
por: Andrés, M V, et al.
Publicado: (2000)

Exploring the dipole polarizability of $^{11}$Li at REX-ISOLDE
por: García-Borge, M J, et al.
Publicado: (2001)

Representation of the QM Subsystem for Long-Range Electrostatic Interaction in Non-Periodic Ab Initio QM/MM Calculations
por: Pan, Xiaoliang, et al.
Publicado: (2018)

From crystallographic data to the solution structure of photoreceptors: the case of the AppA BLUF domain
por: Hashem, Shaima, et al.
Publicado: (2021)

Chemical accuracy in QM/MM calculations on enzyme-catalysed reactions
por: Mulholland, Adrian J
Publicado: (2007)

QM/MM Molecular Dynamics Studies of Metal Binding Proteins
por: Vidossich, Pietro, et al.
Publicado: (2014)

Projected Hybrid Orbitals: A General QM/MM Method
por: Wang, Yingjie, et al.
Publicado: (2014)

Cannot write session to /tmp/vufind_sessions/sess_50kc7ppu9b8qhi5df3nl3m49oa