Classical electrostatics for biomolecular simulations
Classical atomistic simulations, also known as molecular mechanics simulations, use simple
potential-energy functions to model molecular systems at the atomic level. In this …
potential-energy functions to model molecular systems at the atomic level. In this …
Atomistic simulations of membrane ion channel conduction, gating, and modulation
Membrane ion channels are the fundamental electrical components in the nervous system.
Recent developments in X-ray crystallography and cryo-EM microscopy have revealed what …
Recent developments in X-ray crystallography and cryo-EM microscopy have revealed what …
Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability: theory and applications
A current emphasis in empirical force fields is on the development of potential functions that
explicitly treat electronic polarizability. In the present article, the commonly used …
explicitly treat electronic polarizability. In the present article, the commonly used …
High-performance scalable molecular dynamics simulations of a polarizable force field based on classical Drude oscillators in NAMD
W Jiang, DJ Hardy, JC Phillips… - The journal of …, 2011 - ACS Publications
Incorporating the influence of induced polarization in large-scale atomistic molecular
dynamics (MD) simulations is a critical challenge in the progress toward computations of …
dynamics (MD) simulations is a critical challenge in the progress toward computations of …
The Solvation Structure of Na+ and K+ in Liquid Water Determined from High Level ab Initio Molecular Dynamics Simulations
Knowledge of the hydration structure of Na+ and K+ in the liquid phase has wide ranging
implications in the field of biological chemistry. Despite numerous experimental and …
implications in the field of biological chemistry. Despite numerous experimental and …
Biomolecular electrostatics and solvation: a computational perspective
An understanding of molecular interactions is essential for insight into biological systems at
the molecular scale. Among the various components of molecular interactions, electrostatics …
the molecular scale. Among the various components of molecular interactions, electrostatics …
Hydration structure of salt solutions from ab initio molecular dynamics
Cl− ions in aqueous solution have been investigated using density functional theory (DFT)
based Car-Parrinello (CP) molecular dynamics (MD) simulations. CPMD trajectories were …
based Car-Parrinello (CP) molecular dynamics (MD) simulations. CPMD trajectories were …
Ion selectivity in channels and transporters
© 2011 Roux et al. This article is distributed under the terms of an Attribution–
Noncommercial–Share Alike–No Mirror Sites license for the first six months after the …
Noncommercial–Share Alike–No Mirror Sites license for the first six months after the …
Absolute proton hydration free energy, surface potential of water, and redox potential of the hydrogen electrode from first principles: QM/MM MD free-energy …
TS Hofer, PH Hünenberger - The Journal of chemical physics, 2018 - pubs.aip.org
Authors to whom correspondence should be addressed. T. Hofer@ uibk. ac. at, Tel.:+ 43 512
507 57111, Fax:+ 43 512 507 57199 and phil@ igc. phys. chem. ethz. ch, Tel.:+ 41 44 632 …
507 57111, Fax:+ 43 512 507 57199 and phil@ igc. phys. chem. ethz. ch, Tel.:+ 41 44 632 …
Molecular modeling of water-in-salt electrolytes: A comprehensive analysis of polarization effects and force field parameters in molecular dynamics simulations
Accurate modeling of highly concentrated aqueous solutions, such as water-in-salt (WiS)
electrolytes in battery applications, requires proper consideration of polarization …
electrolytes in battery applications, requires proper consideration of polarization …