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Theoretical and Computational Chemistry

Working Paper

Atomistic simulations of dopamine diffusion dynamics on a pristine graphene surface

Qizhang Jia, Cheng Yang, B. Jill Venton, Kateri H. DuBay

Version 1 posted 22 October 2021

317

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Theoretical and Computational Chemistry

Working Paper

Static and Dynamic Statistical Correlations in Water: Comparison of Classical Ab Initio Molecular Dynamics at Elevated Temperature With Path Integral Simulations at Ambient Temperature

Chenghan Li, Francesco Paesani, Gregory A. Voth

Version 2 posted 07 January 2022

936

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Theoretical and Computational Chemistry

Working Paper

INAQS, a generic interface for non-adiabatic QM/MM dynamics: Design, implementation, and validation for GROMACS/Q-CHEM simulations

Vale Cofer-Shabica, Maximilian Menger, Qi Ou, Yihan Shao, Joseph Subotnik, Shirin Faraji

Version 1 posted 02 March 2022

187

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1

Citations

Biological and Medicinal Chemistry

Working Paper

Automated relative binding free energy calculations: from SMILES to ΔΔG

Harry Moore, Christian Margreitter, Jon Paul Janet, Ola Engkvist, Bert de Groot, Vytautas Gapsys

Version 1 posted 25 August 2022

1,271

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Chemical Engineering and Industrial Chemistry

Working Paper

Molecular Dynamics and Network Analysis Reveal the Contrasting Roles of Polar Solutes Within Organic Phase Amphiphile Aggregation

Biswajit Sadhu, Aurora E. Clark

Version 3 posted 28 January 2022

509

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Theoretical and Computational Chemistry

Working Paper

Combinatorial library screening of quinadoline B derivatives against SARS-CoV-2 RNA-dependent RNA polymerase

simone brogi, Mark Tristan Quimque, Kin Israel Notarte, Jeremiah Gabriel Africa, Jenina Beatriz Hernandez, Sophia Morgan Tan, Vincenzo Calderone, Allan Patrick Macabeo

Version 1 posted 22 December 2021

204

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1

Citations

Theoretical and Computational Chemistry

Working Paper

Chemical Space Exploration with Active Learning and Alchemical Free Energies

Yuriy Khalak, Gary Tresadern, David F. Hahn, Bert L. de Groot, Vytautas Gapsys

Version 1 posted 13 July 2022

512

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Physical Chemistry

Working Paper

Does Explicit Polarizability Improve Molecular Dynamics Predictions of Glass Transition Temperatures of Ionic Liquids?

Martin Klajmon, Ctirad Cervinka

Version 1 posted 27 January 2022

150

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Theoretical and Computational Chemistry

Working Paper

BAT2: An open-source tool for flexible, automated and low cost absolute binding free energy calculations

Germano Heinzelmann, David Huggins, Michael Gilson

Version 2 posted 22 February 2024

898

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Theoretical and Computational Chemistry

Working Paper

An automated Calculation Pipeline for Differential Pair Interaction Energies with Molecular Force Fields using the Tinker Molecular Modeling Package

Felix Bänsch, Mirco Daniel, Harald Lanig, Christoph Steinbeck, Achim Zielesny

Version 1 posted 08 February 2024

196

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41 results in Molecular Dynamics in Keywords: Molecular Dynamics

Atomistic simulations of dopamine diffusion dynamics on a pristine graphene surface

Static and Dynamic Statistical Correlations in Water: Comparison of Classical Ab Initio Molecular Dynamics at Elevated Temperature With Path Integral Simulations at Ambient Temperature

INAQS, a generic interface for non-adiabatic QM/MM dynamics: Design, implementation, and validation for GROMACS/Q-CHEM simulations

Automated relative binding free energy calculations: from SMILES to ΔΔG

Molecular Dynamics and Network Analysis Reveal the Contrasting Roles of Polar Solutes Within Organic Phase Amphiphile Aggregation

Combinatorial library screening of quinadoline B derivatives against SARS-CoV-2 RNA-dependent RNA polymerase

Chemical Space Exploration with Active Learning and Alchemical Free Energies

Does Explicit Polarizability Improve Molecular Dynamics Predictions of Glass Transition Temperatures of Ionic Liquids?

BAT2: An open-source tool for flexible, automated and low cost absolute binding free energy calculations

An automated Calculation Pipeline for Differential Pair Interaction Energies with Molecular Force Fields using the Tinker Molecular Modeling Package

41 results in Keywords: Molecular Dynamics