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Physical Chemistry

Working Paper

Accelerated Computation of Free Energy Profile at Ab Initio QM/MM Accuracy via a Semi-Empirical Reference-Potential. III. Gaussian Smoothing on Density-of-States

Wenxin Hu, Pengfei Li, Jia-Ning Wang, Yuanfei Xue, Yan Mo, Jun Zheng, Xiaoliang Pan, Yihan Shao, Ye Mei

Version 1 posted 29 July 2020

294

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Biological and Medicinal Chemistry

Working Paper

A Conserved Asparagine in a Ubiquitin Conjugating Enzyme Positions the Substrate for Nucleophilic Attack

Walker M. Jones, Aaron G. Davis, R. Hunter Wilson, Katherine L. Elliott, Isaiah Sumner

Version 1 posted 29 August 2018

711

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1

Citations

Theoretical and Computational Chemistry

Working Paper

Solvent Effects and pH Dependence of the X-ray Absorption Spectra of Proline from Electrostatic Embedding Quantum Mechanics/Molecular Mechanics and Mixed-Reference Spin-Flip Time-Dependent Density-Functional Theory

Marc ALÍAS RODRÍGUEZ, Simone Bonfrate, Woojin Park, Nicolas Ferré, Cheol Ho Choi, Miquel Huix-Rotllant

Version 2 posted 19 September 2023

215

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Theoretical and Computational Chemistry

Working Paper

A Computational Comparison Between Pomotrelvir and Nirmatrelvir Binding and Reactivity with SARS-CoV-2 Main Protease. Implications for Resistance Mechanisms

Johanna Schillings, Carlos A. Ramos-Guzmán, J. Javier Ruiz-Pernía, Iñaki Tuñón

Version 1 posted 17 January 2024

211

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Theoretical and Computational Chemistry

Working Paper

The Development of the QM/MM Interface and Its Application for the on-the-fly QM/MM Nonadiabatic Dynamics in JADE Package: Theory, Implementation and Applications

Haiyi Huang, Jiawei Peng, Feng Long Gu, Zhenggang Lan, Chao Xu

Version 1 posted 18 March 2024

231

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Theoretical and Computational Chemistry

Working Paper

Simulations of DNA-coordinated light emission vs. intramolecular electron transfer: electron donor-acceptor systems with benzo[a]pyrene derivatives

Widana Kaushalya, Alice Walker

Version 1 posted 30 August 2023

73

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Physical Chemistry

Working Paper

Seamless integration of GEM, a density based-force field, for QM/MM simulations via LICHEM, Psi4 and Tinker-HP

Jorge Nochebuena, Andrew C. Simmonett, G. Andrés Cisneros

Version 1 posted 30 January 2024

136

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Theoretical and Computational Chemistry

Working Paper

Analytic gradients for the electrostatic embedding QM/MM in periodic boundary conditions using particle-mesh Ewald sums and electrostatic potential fitted charge operators

Simone Bonfrate, Nicolas Ferré, Miquel Huix-Rotllant

Version 1 posted 20 February 2024

262

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1

Citations

Theoretical and Computational Chemistry

Working Paper

emle-engine: a flexible electrostatic machine learning embedding package for multiscale molecular dynamics simulations

Kirill Zinovjev, Lester Hedges, Rubén Montagud Andreu, Christopher Woods, Iñaki Tuñón, Marc W. van der Kamp

Version 2 posted 27 February 2024

682

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Theoretical and Computational Chemistry

Working Paper

Assessment of embedding schemes in a hybrid machine learning/classical potentials (ML/MM) scheme

Juan Santiago Grassano, Jonathan Alexis Semelak, Ignacio Javier Pickering, Roitberg Adrian, Mariano Camilo Gonzalez Lebrero, Estrin Dario Ariel

Version 1 posted 22 November 2023

455

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Refine Search

152 results in qm/mm in Keywords: qm/mm

Accelerated Computation of Free Energy Profile at Ab Initio QM/MM Accuracy via a Semi-Empirical Reference-Potential. III. Gaussian Smoothing on Density-of-States

A Conserved Asparagine in a Ubiquitin Conjugating Enzyme Positions the Substrate for Nucleophilic Attack

Solvent Effects and pH Dependence of the X-ray Absorption Spectra of Proline from Electrostatic Embedding Quantum Mechanics/Molecular Mechanics and Mixed-Reference Spin-Flip Time-Dependent Density-Functional Theory

A Computational Comparison Between Pomotrelvir and Nirmatrelvir Binding and Reactivity with SARS-CoV-2 Main Protease. Implications for Resistance Mechanisms

The Development of the QM/MM Interface and Its Application for the on-the-fly QM/MM Nonadiabatic Dynamics in JADE Package: Theory, Implementation and Applications

Simulations of DNA-coordinated light emission vs. intramolecular electron transfer: electron donor-acceptor systems with benzo[a]pyrene derivatives

Seamless integration of GEM, a density based-force field, for QM/MM simulations via LICHEM, Psi4 and Tinker-HP

Analytic gradients for the electrostatic embedding QM/MM in periodic boundary conditions using particle-mesh Ewald sums and electrostatic potential fitted charge operators

emle-engine: a flexible electrostatic machine learning embedding package for multiscale molecular dynamics simulations

Assessment of embedding schemes in a hybrid machine learning/classical potentials (ML/MM) scheme

152 results in Keywords: qm/mm