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11 results in Keywords: Steered Molecular Dynamics

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

647

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Citations

Physical Chemistry

Working Paper

Comparison of Umbrella Sampling and Steered Molecular Dynamics Methods for Computing Free Energy Profiles of Aromatic Substrates through Phospholipid Bilayers

Sang Noh, Rebecca Notman

Version 3 posted 13 May 2020

1,658

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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

1,180

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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

1,325

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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

1,660

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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

498

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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

455

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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

1,206

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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

182

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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

173

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

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

Comparison of Umbrella Sampling and Steered Molecular Dynamics Methods for Computing Free Energy Profiles of Aromatic Substrates through Phospholipid Bilayers

Determination of Base Flipping Free Energy Landscapes from Nonequilibrium Stratification

BAR-based Optimum Adaptive Steered MD for Configurational Sampling

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

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

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

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

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

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

11 results in Keywords: Steered Molecular Dynamics