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Theoretical and Computational Chemistry

Working Paper

BAR-based Optimum Adaptive Steered MD for Configurational Sampling

Xiaohui Wang, Xingzhao Tu, Boming Deng, John Z. H. Zhang, Zhaoxi Sun

Version 2 posted 10 January 2019

1,311

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Physical Chemistry

Working Paper

Determination of Base Flipping Free Energy Landscapes from Nonequilibrium Stratification

Xiaohui Wang, Zhaoxi Sun

Version 2 posted 21 March 2019

1,141

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Biological and Medicinal Chemistry

Working Paper

Thermodynamic Insights of Base Flipping in TNA Duplex: Force Fields, Salt Concentrations, and Free Energy Simulation Methods

Zhaoxi Sun, John Z. H. Zhang

Version 1 posted 02 January 2020

624

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1

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Biological and Medicinal Chemistry

Working Paper

Steered Molecular Dynamics Study of the Age-related Stiffening of the Crystalline Lens

Ewa Golas, Leslie Glasser, Harold A. Scheraga

Version 1 posted 17 January 2022

152

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Theoretical and Computational Chemistry

Working Paper

The Local Environment of Iron Determines the Rupture Force of Rubredoxin and Not Hydrogen Bond Networks

Maximilian Scheurer, Andreas Dreuw, Martin Head-Gordon, Tim Stauch

Version 1 posted 20 April 2020

503

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Physical Chemistry

Working Paper

BAR-Based Multi-Dimensional Nonequilibrium Pulling for Indirect Construction of QM/MM Free Energy Landscape

Xiaohui Wang, Qiaole He, Zhaoxi Sun

Version 2 posted 08 March 2019

1,197

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Theoretical and Computational Chemistry

Working Paper

Seeding the Multi-dimensional Nonequilibrium Pulling for Hamiltonian Variation: Indirect Nonequilibrium Free Energy Simulations at QM levels

Zhaoxi Sun, Qiaole He

Version 2 posted 04 October 2021

412

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Theoretical and Computational Chemistry

Working Paper

Massively Parallel Implementation of Steered Molecular Dynamics in Tinker-HP: Comparisons of Polarizable and Non-Polarizable Simulations of Realistic Systems

Frédéric Célerse, Louis Lagardere, Étienne Derat, Jean-Philip Piquemal

Version 2 posted 24 April 2019

1,609

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Theoretical and Computational Chemistry

Working Paper

Exploring ssDNA translocation through alpha-hemolysin using Coarse-Grained Steered Molecular Dynamics

Cagla Okyay, Delphine Dessaux, Rosa Ramirez, Jérôme Mathé, Nathalie Basdevant

Version 1 posted 08 April 2024

86

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Physical Chemistry

Working Paper

BAR-based Multi-dimensional Nonequilibrium Pulling for Indirect Construction of QM/MM Free Energy Landscapes: Varying the QM Region

Zhaoxi Sun, Zhirong Liu

Version 3 posted 30 March 2021

462

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11 results in Steered Molecular Dynamics in Keywords: Steered Molecular Dynamics

BAR-based Optimum Adaptive Steered MD for Configurational Sampling

Determination of Base Flipping Free Energy Landscapes from Nonequilibrium Stratification

Thermodynamic Insights of Base Flipping in TNA Duplex: Force Fields, Salt Concentrations, and Free Energy Simulation Methods

Steered Molecular Dynamics Study of the Age-related Stiffening of the Crystalline Lens

The Local Environment of Iron Determines the Rupture Force of Rubredoxin and Not Hydrogen Bond Networks

BAR-Based Multi-Dimensional Nonequilibrium Pulling for Indirect Construction of QM/MM Free Energy Landscape

Seeding the Multi-dimensional Nonequilibrium Pulling for Hamiltonian Variation: Indirect Nonequilibrium Free Energy Simulations at QM levels

Massively Parallel Implementation of Steered Molecular Dynamics in Tinker-HP: Comparisons of Polarizable and Non-Polarizable Simulations of Realistic Systems

Exploring ssDNA translocation through alpha-hemolysin using Coarse-Grained Steered Molecular Dynamics

BAR-based Multi-dimensional Nonequilibrium Pulling for Indirect Construction of QM/MM Free Energy Landscapes: Varying the QM Region

11 results in Keywords: Steered Molecular Dynamics