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Darrin M. York
Darrin M. York
Henry Rutgers University Professor, Rutgers University
Verified email at rutgers.edu - Homepage
Title
Cited by
Cited by
Year
Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems
T Darden, D York, L Pedersen
The Journal of chemical physics 98 (12), 10089-10092, 1993
300191993
CHARMM: the biomolecular simulation program
BR Brooks, CL Brooks III, AD Mackerell Jr, L Nilsson, RJ Petrella, B Roux, ...
Journal of computational chemistry 30 (10), 1545-1614, 2009
87692009
Amber 2021
DA Case, HM Aktulga, K Belfon, I Ben-Shalom, SR Brozell, DS Cerutti, ...
University of California, San Francisco, 2021
54682021
The effect of long‐range electrostatic interactions in simulations of macromolecular crystals: A comparison of the Ewald and truncated list methods
DM York, TA Darden, LG Pedersen
The Journal of chemical physics 99 (10), 8345-8348, 1993
9611993
A smooth solvation potential based on the conductor-like screening model
DM York, M Karplus
The Journal of Physical Chemistry A 103 (50), 11060-11079, 1999
4911999
GPU-accelerated molecular dynamics and free energy methods in Amber18: performance enhancements and new features
TS Lee, DS Cerutti, D Mermelstein, C Lin, S LeGrand, TJ Giese, ...
Journal of chemical information and modeling 58 (10), 2043-2050, 2018
3562018
Extension of the self-consistent-charge density-functional tight-binding method: third-order expansion of the density functional theory total energy and introduction of a …
Y Yang, H Yu, D York, Q Cui, M Elstner
The Journal of Physical Chemistry A 111 (42), 10861-10873, 2007
3212007
An efficient linear-scaling Ewald method for long-range electrostatic interactions in combined QM/MM calculations
K Nam, J Gao, DM York
Journal of Chemical Theory and Computation 1 (1), 2-13, 2005
3192005
A chemical potential equalization method for molecular simulations
DM York, W Yang
The Journal of chemical physics 104 (1), 159-172, 1996
2751996
Constant pH replica exchange molecular dynamics in explicit solvent using discrete protonation states: implementation, testing, and validation
JM Swails, DM York, AE Roitberg
Journal of chemical theory and computation 10 (3), 1341-1352, 2014
2642014
AMBER 2018, University of California, San Francisco, 2018
DA Case, JT Berryman, RM Betz, DS Cerutti, TE Cheatham III, TA Darden, ...
There is no corresponding record for this reference, 2015
2502015
Atomic-level accuracy in simulations of large protein crystals.
DM York, A Wlodawer, LG Pedersen, TA Darden
Proceedings of the National Academy of Sciences 91 (18), 8715-8718, 1994
2341994
Alchemical binding free energy calculations in AMBER20: Advances and best practices for drug discovery
TS Lee, BK Allen, TJ Giese, Z Guo, P Li, C Lin, TD McGee Jr, ...
Journal of Chemical Information and Modeling 60 (11), 5595-5623, 2020
2312020
Linear‐scaling semiempirical quantum calculations for macromolecules
TS Lee, DM York, W Yang
The Journal of Chemical Physics 105 (7), 2744-2750, 1996
2211996
Toward the accurate modeling of DNA: the importance of long-range electrostatics
DM York, W Yang, H Lee, T Darden, LG Pedersen
Journal of the American Chemical Society 117 (17), 5001-5002, 1995
2211995
AmberTools
DA Case, HM Aktulga, K Belfon, DS Cerutti, GA Cisneros, VWD Cruzeiro, ...
Journal of chemical information and modeling 63 (20), 6183-6191, 2023
2192023
Specific reaction parametrization of the AM1/d Hamiltonian for phosphoryl transfer reactions: H, O, and P atoms
K Nam, Q Cui, J Gao, DM York
Journal of Chemical Theory and Computation 3 (2), 486-504, 2007
1722007
Using AMBER18 for relative free energy calculations
LF Song, TS Lee, C Zhu, DM York, KM Merz Jr
Journal of chemical information and modeling 59 (7), 3128-3135, 2019
1672019
Accurate proton affinity and gas-phase basicity values for molecules important in biocatalysis
A Moser, K Range, DM York
The Journal of Physical Chemistry B 114 (43), 13911-13921, 2010
1662010
The fast Fourier Poisson method for calculating Ewald sums
D York, W Yang
Journal of Chemical Physics 101 (4), 3298-3300, 1994
1651994
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Articles 1–20