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A simple polarizable model of water based on classical Drude oscillators
A simple polarizable water model is developed and optimized for molecular dynamics simulations of the liquid phase under ambient conditions. The permanent charge distribution of the water molecule isExpand
Modeling induced polarization with classical Drude oscillators: Theory and molecular dynamics simulation algorithm
A simple treatment for incorporating induced polarization in computer simulations is formulated on the basis of the classical Drude oscillator model. In this model, electronic induction isExpand
Deep convolutional networks for quality assessment of protein folds
It is shown that deep convolutional networks can be used to predict the ranking of model structures solely on the basis of their raw three-dimensional atomic densities, without any feature tuning. Expand
A polarizable model of water for molecular dynamics simulations of biomolecules
The SWM4-DP polarizable water model [G. Lamoureux, A.D. MacKerell, Jr., B. Roux, J. Chem. Phys. 119 (2003) 5185], based on classical Drude oscillators, is re-optimized for negatively charged DrudeExpand
Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field.
Structural and dynamic properties of the resulting ion models in aqueous solutions at infinite dilution are presented. Expand
Determination of Electrostatic Parameters for a Polarizable Force Field Based on the Classical Drude Oscillator.
This study confirms the feasibility of the use of a polarizable force field based on a classical Drude model for simulations of biomolecules in the condensed phase. Expand
Transport mechanisms in the ammonium transporter family.
Functional experiments on plant ammonium transporters and rhesus proteins suggest a variety of permeation mechanisms including the passive diffusion of NH(3), the antiport ofNH(4)(+)/H(+), the transport of NH)(+), or the cotransport of NH (3)/H (+). Expand
Absolute hydration free energy scale for alkali and halide ions established from simulations with a polarizable force field.
A polarizable potential function for the hydration of alkali and halide ions is developed on the basis of the recent SWM4-DP water model, which corresponds to an absolute scale in which the intrinsic hydration free energy of the proton is -247 kcal/mol. Expand
Molecular dynamics study of hydration in ethanol-water mixtures using a polarizable force field.
To investigate the structural organization of hydrophobic hydration in water-ethanol mixtures, molecular dynamics simulations based on detailed atomic models are used and the calculated dielectric constant for the various water-alcohol mixtures is in excellent agreement with experimental data. Expand
Peptide Hydrolysis in Thermolysin:  Ab Initio QM/MM Investigation of the Glu143-Assisted Water Addition Mechanism.
The present simulations give further evidence that Glu143 is a highly effective proton shuttle which should be assigned a key role in any reaction mechanism proposed for TLN. Expand