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Theoretical and Computational Chemistry

Working Paper

Parameterization of general organic polymers within the Open Force Field framework

Connor M. Davel, Timotej Bernat, Jeffrey R. Wagner, Michael R. Shirts

Version 2 posted 19 October 2023

586

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Theoretical and Computational Chemistry

Working Paper

Expanded Ensemble Methods Can Be Used to Accurately Predict Protein-Ligand Relative Binding Free Energies

Si Zhang, David Hahn, Michael R. Shirts, Vincent Voelz

Version 1 posted 26 May 2021

432

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Theoretical and Computational Chemistry

Working Paper

Testing for Physical Validity in Molecular Simulations

Pascal T. Merz, Michael R. Shirts

Version 2 posted 24 July 2018

953

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Theoretical and Computational Chemistry

Working Paper

Toward Learned Chemical Perception of Force Field Typing Rules

Camila Zanette, Caitlin C. Bannan, Christopher I. Bayly, Josh Fass, Michael Gilson, Michael R. Shirts, John Chodera, David Mobley

Version 3 posted 15 October 2018

1,315

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Theoretical and Computational Chemistry

Working Paper

Using physical property surrogate models to perform multi-fidelity global optimization of force field parameters

Owen Madin, Michael Shirts

Version 2 posted 09 December 2022

352

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Theoretical and Computational Chemistry

Working Paper

Development and Benchmarking of Open Force Field 2.0.0 — the Sage Small Molecule Force Field

Simon Boothroyd, Pavan Kumar Behara, Owen Madin, David Hahn, Hyesu Jang, Vytautas Gapsys, Jeffrey Wagner, Joshua Horton, David Dotson, Matthew Thompson, Jessica Maat, Trevor Gokey, Lee-Ping Wang, Daniel Cole, Michael Gilson, John Chodera, Christopher Bayly, Michael Shirts, David Mobley

Version 2 posted 10 January 2023

1,467

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2

Citations

Theoretical and Computational Chemistry

Working Paper

Improving force field accuracy by training against condensed phase mixture properties

Simon Boothroyd, Owen Madin, David Mobley, Lee-Ping Wang, John Chodera, Michael Shirts

Version 3 posted 15 April 2022

775

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Theoretical and Computational Chemistry

Working Paper

Folding Coarse-Grained Oligomer Models with PyRosetta

Theodore L. Fobe, Christopher C. Walker, Garrett A. Meek, Michael R. Shirts

Version 2 posted 19 May 2022

457

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Theoretical and Computational Chemistry

Working Paper

The Open Force Field Evaluator: An automated, efficient, and scalable framework for the estimation of physical properties from molecular simulation

Simon Boothroyd, Lee-Ping Wang, David Mobley, John Chodera, Michael Shirts

Version 1 posted 05 August 2021

748

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1

Citations

Theoretical and Computational Chemistry

Working Paper

Obtaining and characterizing stable bicontinuous cubic morphologies and their nanochannels in lyotropic liquid crystal membranes

Subin Sahu, Nathanael Schwindt, Benjamin Coscia, Michael Shirts

Version 1 posted 02 September 2022

297

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16 results in Michael Shirts in Authors: Michael Shirts

Parameterization of general organic polymers within the Open Force Field framework

Expanded Ensemble Methods Can Be Used to Accurately Predict Protein-Ligand Relative Binding Free Energies

Testing for Physical Validity in Molecular Simulations

Toward Learned Chemical Perception of Force Field Typing Rules

Using physical property surrogate models to perform multi-fidelity global optimization of force field parameters

Development and Benchmarking of Open Force Field 2.0.0 — the Sage Small Molecule Force Field

Improving force field accuracy by training against condensed phase mixture properties

Folding Coarse-Grained Oligomer Models with PyRosetta

The Open Force Field Evaluator: An automated, efficient, and scalable framework for the estimation of physical properties from molecular simulation

Obtaining and characterizing stable bicontinuous cubic morphologies and their nanochannels in lyotropic liquid crystal membranes

16 results in Authors: Michael Shirts