Publications by authors named "Jason Swails"

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Recent Developments in Amber Biomolecular Simulations.
David A Case, David S Cerutti, Vinícius Wilian D Cruzeiro, Thomas A Darden, Robert E Duke, Jason Swails

J Chem Inf Model· August 2025

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OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials.
Peter Eastman, Raimondas Galvelis, Raúl P Peláez, Charlles R A Abreu, Stephen E Farr, Jason Swails

J Phys Chem B· January 2024

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OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials.
Peter Eastman, Raimondas Galvelis, Raúl P Peláez, Charlles R A Abreu, Stephen E Farr, Jason Swails

ArXiv· November 2023

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AmberTools.
David A Case, Hasan Metin Aktulga, Kellon Belfon, David S Cerutti, G Andrés Cisneros, Jason Swails

J Chem Inf Model· October 2023

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Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix.
Nigel W Moriarty, Pawel A Janowski, Jason M Swails, Hai Nguyen, Jane S Richardson

Acta Crystallogr D Struct Biol· January 2020

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A Coupled Ionization-Conformational Equilibrium Is Required To Understand the Properties of Ionizable Residues in the Hydrophobic Interior of Staphylococcal Nuclease.
Jinfeng Liu, Jason Swails, John Z H Zhang, Xiao He, Adrian E Roitberg

J Am Chem Soc· February 2018

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Improved Accuracy for Constant pH-REMD Simulations through Modification of Carboxylate Effective Radii.
Andrew V Yeager, Jason M Swails, Bill R Miller

J Chem Theory Comput· October 2017

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Erratum to: Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset.
Michael R Shirts, Christoph Klein, Jason M Swails, Jian Yin, Michael K Gilson

J Comput Aided Mol Des· August 2017

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OpenMM 7: Rapid development of high performance algorithms for molecular dynamics.
Peter Eastman, Jason Swails, John D Chodera, Robert T McGibbon, Yutong Zhao

PLoS Comput Biol· July 2017

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Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset.
Michael R Shirts, Christoph Klein, Jason M Swails, Jian Yin, Michael K Gilson

J Comput Aided Mol Des· January 2017

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Advanced Potential Energy Surfaces for Molecular Simulation.
Alex Albaugh, Henry A Boateng, Richard T Bradshaw, Omar N Demerdash, Jacek Dziedzic, Jason Swails

J Phys Chem B· September 2016

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CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field.
Jumin Lee, Xi Cheng, Jason M Swails, Min Sun Yeom, Peter K Eastman

J Chem Theory Comput· January 2016

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AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules.
Jason Swails, Tong Zhu, Xiao He, David A Case

J Biomol NMR· October 2015

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MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories.
Robert T McGibbon, Kyle A Beauchamp, Matthew P Harrigan, Christoph Klein, Jason M Swails

Biophys J· October 2015

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Interpretation of pH-activity profiles for acid-base catalysis from molecular simulations.
Thakshila Dissanayake, Jason M Swails, Michael E Harris, Adrian E Roitberg, Darrin M York

Biochemistry· February 2015

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Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation.
Jason M Swails, Darrin M York, Adrian E Roitberg

J Chem Theory Comput· March 2014

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Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide.
Christina Bergonzo, Niel M Henriksen, Daniel R Roe, Jason M Swails, Adrian E Roitberg

J Chem Theory Comput· January 2014

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SPAM: A Simple Approach for Profiling Bound Water Molecules.
Guanglei Cui, Jason M Swails, Eric S Manas

J Chem Theory Comput· December 2013

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Enhancing Conformation and Protonation State Sampling of Hen Egg White Lysozyme Using pH Replica Exchange Molecular Dynamics.
Jason M Swails, Adrian E Roitberg

J Chem Theory Comput· November 2012

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MMPBSA.py: An Efficient Program for End-State Free Energy Calculations.
Bill R Miller, T Dwight McGee, Jason M Swails, Nadine Homeyer, Holger Gohlke

J Chem Theory Comput· September 2012

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pH-dependent mechanism of nitric oxide release in nitrophorins 2 and 4.
Jason M Swails, Yilin Meng, F Ann Walker, Marcelo A Marti, Dario A Estrin

J Phys Chem B· January 2009

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