Darrin M. York

GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features

J. Chem. Inf. Model., (2018) 58, 2043-2050
DOI: 10.1021/acs.jcim.8b00462

A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes

Molecules, (2018) 23, 2695-2719
DOI: 10.3390/molecules23102695

On the convergence of multi-scale free energy simulations

Mol Simul, (2018) 44, 1062-1081
DOI: 10.1080/08927022.2018.1475741

A GPU-Accelerated Parameter Interpolation Thermodynamic Integration Free Energy Method

J. Chem. Theory Comput., (2018) 14, 1564–1582
DOI: 10.1021/acs.jctc.7b01175 Download PDF

Model for the Functional Active State of the TS Ribozyme from Molecular Simulation

Agnew. Chem. Int. Ed., (2017) 56, 13392-13395
DOI: 10.1002/anie.201705608 Download PDF

Quantum mechanical force fields for condensed phase molecular simulations

J. Phys.: Condens. Matter, (2017) 29, 383002-383016
DOI: 10.1088/1361-648X/aa7c5c Download PDF

A Multidimensional B-Spline Correction for Accurate Modeling Sugar Puckering in QM/MM Simulations

J. Chem. Theory Comput., (2017) 13, 3975-3984
DOI: 10.1021/acs.jctc.7b00161 Download PDF

Toward Fast and Accurate Binding Affinity Prediction with pmemdGTI: An Efficient Implementation of GPU-Accelerated Thermodynamic Integration

J. Chem. Theory Comput. , (2017) 13, 3077-3084
DOI: 10.1021/acs.jctc.7b00102 Download PDF

Divalent Metal Ion Activation of a Guanine General Base in the Hammerhead Ribozyme: Insights from Molecular Simulations

Biochemistry, (2017) 56, 2985-2994
DOI: 10.1021/acs.biochem.6b01192 Download PDF

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