עקוב אחר
Darrin M. York
Darrin M. York
Henry Rutgers University Professor, Rutgers University
כתובת אימייל מאומתת בדומיין rutgers.edu - דף הבית
כותרת
צוטט על ידי
צוטט על ידי
שנה
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
310211993
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
91082009
Amber 2021
DA Case, HM Aktulga, K Belfon, I Ben-Shalom, SR Brozell, DS Cerutti, ...
University of California, San Francisco, 2021
57332021
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
9821993
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
5081999
AmberTools
DA Case, HM Aktulga, K Belfon, DS Cerutti, GA Cisneros, VWD Cruzeiro, ...
Journal of chemical information and modeling 63 (20), 6183-6191, 2023
4272023
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
3842018
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
3322005
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
3252007
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
2792014
A chemical potential equalization method for molecular simulations
DM York, W Yang
The Journal of chemical physics 104 (1), 159-172, 1996
2791996
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
2652020
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
2542015
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
2361994
Linear‐scaling semiempirical quantum calculations for macromolecules
TS Lee, DM York, W Yang
The Journal of Chemical Physics 105 (7), 2744-2750, 1996
2221996
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
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
1862019
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
1772007
DeePMD-kit v2: A software package for deep potential models
J Zeng, D Zhang, D Lu, P Mo, Z Li, Y Chen, M Rynik, L Huang, Z Li, S Shi, ...
The Journal of Chemical Physics 159 (5), 2023
1762023
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
1742010
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מאמרים 1–20