Related papers: Non-conformal coarse-grained potentials for water
[ This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. This article appeared in The Journal of Chemical Physics, 157, 024504 (2022) and may be found at:…
The isothermal compressibility of water is essential to understand its anomalous properties. We compute it by ab initio molecular dynamics simulations of 200 molecules at five densities, using two different van der Waals density…
Modern analog computers are ideally suited to solving large systems of ordinary differential equations at high speed with low energy consumtion and limited accuracy. In this article, we survey N-body physics, applied to a simple water model…
In molecular simulations, neural network force fields aim at achieving \emph{ab initio} accuracy with reduced computational cost. This work introduces enhancements to the Deep Potential network architecture, integrating a message-passing…
Aqueous lithium chloride solutions up to very high concentrations were investigated in classical molecular dynamics simulations. Various force fields based on the 12-6 Lennard-Jones model, parametrized for non-polarizable water solvent…
In this work, a two dimensional system of polymer grafted nanoparticles is analyzed using large-scale Langevin Dymanics simulations. Effective core-softened potentials were obtained for two cases: one where the polymers are free to rotate…
Machine learning-based neural network potentials have the ability to provide ab initio-level predictions while reaching large length and time scales often limited to empirical force fields. Traditionally, neural network potentials rely on a…
Machine-learned coarse-grained (CG) models often suffer from noisy training data, limiting their accuracy and transferability. We propose a method to generate low-noise training data based on the potential of mean force by constraining CG…
Despite the simplicity of its molecular unit, water is a challenging system because of its uniquely rich polymorphism and predicted but yet unconfirmed features. Introducing a novel space of generalized coordinates that capture changes in…
Isothermal-isobaric molecular dynamics simulations have been performed to examine a broad set of properties of the model water-1,2-dimethoxyethane (DME) mixture as a function of composition. The SPC-E and TIP4P-Ew water models and the…
Can we avoid molecular dynamics simulations to estimate the electrostatic interaction between charged objects separated by a nanometric distance in water? To answer this question, we develop a continuous model for the dielectric properties…
Coulomb interactions are present in a wide variety of all-atom force fields. Spherical truncations of these interactions permit fast simulations but are problematic due to their incorrect thermodynamics. Herein we demonstrate that simple…
We report a multiscale modeling study for charged cylindrical nanopores using three modeling levels that include (1) an all-atom explicit-water model studied with molecular dynamics (MD), and reduced models with implicit water containing…
Compared to top-down coarse-grained (CG) models, bottom-up approaches are capable of offering higher structural fidelity. This fidelity results from the tight link to a higher-resolution reference, making the CG model chemically specific.…
Water modeling is a challenging problem. Its anomalies are difficult to reproduce, promoting the proliferation of a large number of computational models, among which researchers select the most appropriate for the property they study. In…
I have investigated the structural and dynamic properties of water by performing a series of molecular dynamic simulations in the range of temperatures from 213 K to 360 K, using the Simple Point Charge-Extended (SPC/E) model. I performed…
The dielectric response of nano-confined fluids is crucial across technologies and biological systems, yet its calculation and interpretation from molecular simulations are often muddled by unclear boundary conditions. We re-derive the…
Smooth model potentials with parameters selected to reproduce the spectrum of one-electron atoms are used to approximate the singular Coulomb potential. Even when the potentials do not mimic the Coulomb singularity, much of the spectrum is…
The water/electrode interface under an applied bias potential is a challenging out-of-equilibrium phenomenon, which is difficult to accurately model at the atomic scale. In this study, we employ a combined approach of Density Functional…
Understanding the behavior of biomolecules such as proteins requires understanding the critical influence of the surrounding fluid (solvent) environment--water with mobile salt ions such as sodium. Unfortunately, for many studies, fully…