Publications by authors named "Jason M Swails"

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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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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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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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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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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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