Non-Polarizable Force Field of Water Based on the Dielectric Constant: TIP4P/ε

Fuentes-Azcatl, Raúl; Alejandre, José

doi:10.1021/jp410865y

Cited by 146 publications

(155 citation statements)

References 42 publications

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“…The dielectric constant is extremely relevant to the simulation of biomolecular systems, which was missing in old parameterization techniques due to computational inefficiency. Some of the recent models that were specially designed to reproduce the correct experimental dielectric constants include TIP4P/ ɛ, SPC/ ɛ, H2ODC . The dielectric constant was selected as a target property in the parameterization of OPC, OPC3, TIP3PFB, and TIP4PFB …”

Section: Explicit Water Modelsmentioning

confidence: 99%

“…The need for better accuracy motivates an on‐going search for more accurate yet computationally facile water models. Yet, despite notable recent improvements, models of this class still fail to reproduce all the key properties of liquid water accurately and simultaneously . Life itself depends on several of these properties being precisely what they are .…”

Section: Explicit Water Modelsmentioning

confidence: 99%

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Water models for biomolecular simulations

Onufriev

Izadi²

2017

WIREs Comput Mol Sci

176

225

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Modern simulation and modeling approaches to investigation of biomolecular structure and function rely heavily on a variety of methods—water models—to approximate the influence of solvent. We give a brief overview of several distinct classes of available water models, with the emphasis on the conceptual basis at each level of approximation. The main focus is on classes of models most widely used in atomistic simulations, including popular implicit and explicit solvent models. Among the latter, nonpolarizable N‐point models are covered in most detail, including some recent methodological advances and nuances. Notes on practical availability and usage in biomolecular simulations are included. Atomistic simulations that were hardly possible only a short while ago have revealed significant problems that can be traced to deficiencies of most commonly used N‐point water models. Recently developed models of this class approximate experimental properties of liquid water much closer than before, and show promise in practical biomolecular simulations. Obstacles to wider adoption of these more accurate water models, both technical and conceptual, are discussed. It is argued that verifying robustness of simulation results to the choice of water model can be of immediate benefit even in the absence of a clear replacement for older models; a specific strategy is proposed. The review is concluded with a discussion on how force‐field development efforts can benefit from better solvent models, and vice versa. WIREs Comput Mol Sci 2018, 8:e1347. doi: 10.1002/wcms.1347 This article is categorized under: Structure and Mechanism > Computational Biochemistry and Biophysics Molecular and Statistical Mechanics > Molecular Dynamics and Monte‐Carlo Methods

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Section: Explicit Water Modelsmentioning

confidence: 99%

Section: Explicit Water Modelsmentioning

confidence: 99%

Water models for biomolecular simulations

Onufriev

Izadi²

2017

WIREs Comput Mol Sci

176

225

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“…The TIP4P/ force field [30] used in this work was parametrised to simultaneously reproduce the experimental dielectric constant and temperature of maximum density. The results at 298.15 K of the liquid density of mixtures .…”

Section: Acetamide-water Mixturesmentioning

confidence: 99%

Parametrisation of a force field of acetamide for simulations of the liquid phase

et al. 2015

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Molecular dynamics simulations are performed to develop new parameters for acetamide using a systematic procedure proposed by Salas et al., where the atomic charges were fitted to reproduce the experimental dielectric constant and the Lennard-Jones parameters to match the surface tension and density. The parameters for formamide recently calculated by Pérez et al. were used to obtain the new parameters of acetamide where atoms of the amine group and carbon kept the same intermolecular parameter values in both molecules. The parameters of the methyl group, taken as united atom, and the oxygen atom were fitted to reproduce the dielectric constant, surface tension and density at 358.15 K. The new set of parameters, based on the optimised potential for liquids simulations with all atoms, was able to predict results of the target properties as a function of temperature as a pure component and the dielectric constant and density of binary mixtures with water and formamide as a function of acetamide concentration at 298.15 K. The polymer chains formed by hydrogen bond interactions were analysed to understand the maximum of dielectric constant in acetamide-water mixtures.

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“…The idea is to combine the parametrization method employed for rigid model with the flexibility which adds additional degrees of freedom for the parametrization. We selected the rigid SPC/ǫ 14 as an starting point due to its simplicity and because the rigid model already give some thermodynamic 14 and dynamic properties 15 close to the experimental results at room temperature and pressures.…”

Section: Introductionmentioning

confidence: 99%

“…The parameterization procedure is the same employed in previous publication and goes as follows. 16 ǫ αβ , σ αβ , q α and q β were defined by requiring that the model reproduces: the density of liquid water, dielectric constant and dipole moment at 1 bar and 240K and the melting temperature at 1 bar. The idea behind is approach is to develop a flexible model which reproduces the bulk thermodynamic and dynamic properties of the equivalent rigid model for the pure system, but due to the flexibility is able to provide better results in mixtures or in confined geometries.…”

mentioning

confidence: 99%