scholarly journals Erratum: “Adaptive resolution simulation of a biomolecule and its hydration shell: Structural and dynamical properties” [J. Chem. Phys. 142, 195101 (2015)]

2017 ◽  
Vol 146 (4) ◽  
pp. 049901
Author(s):  
Aoife C. Fogarty ◽  
Raffaello Potestio ◽  
Kurt Kremer
Keyword(s):  
Hydration Shell ◽  
Chem Phys ◽  
Adaptive Resolution ◽  
Dynamical Properties ◽  
Resolution Simulation

scholarly journals Adaptive resolution simulation of a biomolecule and its hydration shell: Structural and dynamical properties

2015 ◽  
Vol 142 (19) ◽  
pp. 195101 ◽  
Author(s):  
Aoife C. Fogarty ◽  
Raffaello Potestio ◽  
Kurt Kremer
Keyword(s):  
Hydration Shell ◽  
Adaptive Resolution ◽  
Dynamical Properties ◽  
Resolution Simulation

scholarly journals Adaptive Resolution Simulation of Supramolecular Water: The Concurrent Making, Breaking, and Remaking of Water Bundles

2016 ◽  
Vol 12 (8) ◽  
pp. 4138-4145 ◽  
Author(s):  
Julija Zavadlav ◽  
Siewert J. Marrink ◽  
Matej Praprotnik
Keyword(s):  
Adaptive Resolution ◽  
Resolution Simulation

scholarly journals Retraction: Atomic-scale simulation to study the dynamical properties and local structure of Cu–Zr and Ni–Zr metallic glass-forming alloys

2016 ◽  
Vol 18 (29) ◽  
pp. 19976-19976 ◽  
Author(s):  
M. H. Yang ◽  
Y. Li ◽  
J. H. Li ◽  
B. X. Liu
Keyword(s):  
Metallic Glass ◽  
Local Structure ◽  
Chem Phys ◽  
Atomic Scale ◽  
Glass Forming ◽  
Dynamical Properties ◽  
Phys Chem Chem Phys

Retraction of ‘Atomic-scale simulation to study the dynamical properties and local structure of Cu–Zr and Ni–Zr metallic glass-forming alloys’ by M. H. Yang et al., Phys. Chem. Chem. Phys., 2016, 18, 7169–7183.

scholarly journals Ab initio QM/MM MD simulations of the hydrated Ca2+ ion

2004 ◽  
Vol 76 (1) ◽  
pp. 37-47 ◽  
Author(s):  
C. F. Schwenk ◽  
B. M. Rode
Keyword(s):  
Density Functional ◽  
Hydration Shell ◽  
Md Simulations ◽  
Distribution Functions ◽  
Quantum Mechanical ◽  
Hartree Fock ◽  
Velocity Autocorrelation ◽  
Exchange Processes ◽  
Hydrate Complex ◽  
Dynamical Properties

The comparison of two different combined quantum mechanical (QM)/molecular mechanical (MM) simulations treating the quantum mechanical region at Hartree-Fock (HF) and B3-LYP density functional theory (DFT) level allowed us to determine structural and dynamical properties of the hydrated calcium ion. The structure is discussed in terms of radial distribution functions, coordination number distributions, and various angular distributions and the dynamical properties, as librations and vibrations, reorientational times and mean residence times were evaluated by means of velocity autocorrelation functions. The QM/MM molecular dynamics (MD) simulation results prove an eightfold-coordinated complex to be the dominant species, yielding average coordination numbers of 7.9 in the HF and 8.0 in the DFT case. Structural and dynamical results show higher rigidity of the hydrate complex using DFT. The high instability of calcium ion's hydration shell allows the observation of water-exchange processes between first and second hydration shell and shows that the mean lifetimes of water molecules in this first shell (<100 ps) have been strongly overestimated by conclusions from experimental data.

Dynamical properties of the hydration shell of fully deuterated myoglobin

2011 ◽  
Vol 84 (4) ◽  
Author(s):  
Klaus Achterhold ◽  
Andreas Ostermann ◽  
Martine Moulin ◽  
Michael Haertlein ◽  
Tobias Unruh ◽  
...  
Keyword(s):  
Hydration Shell ◽  
Dynamical Properties

Adaptive resolution simulation of oligonucleotides

2016 ◽  
Vol 145 (23) ◽  
pp. 234101 ◽  
Author(s):  
Paulo A. Netz ◽  
Raffaello Potestio ◽  
Kurt Kremer
Keyword(s):  
Adaptive Resolution ◽  
Resolution Simulation

Back-mapping augmented adaptive resolution simulation

2020 ◽  
Vol 153 (16) ◽  
pp. 164118
Author(s):  
S. Thaler ◽  
M. Praprotnik ◽  
J. Zavadlav
Keyword(s):  
Adaptive Resolution ◽  
Resolution Simulation
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