Development of a Nonlinear Classical Polarization Model for Liquid Water and Aqueous Solutions: COS/D

Kunz, Anna-Pitschna E.; Gunsteren, Wilfred F. van

doi:10.1021/jp903164s

Cited by 82 publications

(109 citation statements)

References 78 publications

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“…The static dielectric permittivity ε(0) of the polarizable COS/D water model derived from the slope, ignoring large field strengths, is 77.3 ± 0.6 from a total of 34.8 ns of simulation. This is closer to the experimental value [58] of 78.5 than the previously reported [21] Figure 4. Dependence of the polarization averaged over time P z on the applied electric field E ext z for COS/D [21] water.…”

Section: Journal Of Computational Chemistrysupporting

confidence: 85%

“…For certain polarizable models, [20,21] it is necessary to add an additional virtual atomic interaction center M. The position of this virtual site M is defined in the plane of the three nonvirtual atoms i, j, and k,…”

Section: Journal Of Computational Chemistrymentioning

confidence: 99%

“…In addition, the GROMOS simulation software allows the linear dependence of the induced dipole µ µ µ ind,i on the electric field E i to be substituted by a sublinear dependence for large field strengths, [21] which can be achieved by making the polarizability α i electric field dependent. For example, α i is replaced by (25) with V self = i V self,i , where i runs over all polarizable centers.…”

Section: Journal Of Computational Chemistrymentioning

confidence: 99%

“…The use of a quartic instead of a harmonic attractive bond-length potential energy function makes the polarizability nonlinear [21] and has the advantage that overpolarization due to close distances between charges of different molecules is avoided as a result of the superlinear increase of the forces for longer bond lengths. The polarizability of the model resides in the free rotation of the DP particle around the central CP site and the oscillation of the 346 http://wileyonlinelibrary.com/jcc…”

Section: Coarse-grained Supramolecular Force Field Termsmentioning

confidence: 99%

“…[21] For the calculation of the dielectric permittivity, a cubic box with an edge length of 3.1057 nm was filled with 1000 COS/D [21] water molecules, resulting in a density of 997 kg/m 3 , corresponding to the density of liquid water at 298 K and 1 atm. [60] For the…”

Section: Mixtures Of Coarse-grained Dmso or Meoh And Coarse-grained Wmentioning

confidence: 99%

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New functionalities in the GROMOS biomolecular simulation software

Kunz¹,

Allison²,

Geerke³

et al. 2011

J Comput Chem

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105

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Since the most recent description of the functionalities of the GROMOS software for biomolecular simulation in 2005 many new functions have been implemented. In this article, the new functionalities that involve modified forces in a molecular dynamics (MD) simulation are described: the treatment of electronic polarizability, an implicit surface area and internal volume solvation term to calculate interatomic forces, functions for the GROMOS coarse-grained supramolecular force field, a multiplicative switching function for nonbonded interactions, adiabatic decoupling of a number of degrees of freedom with temperature or force scaling to enhance sampling, and nonequilibrium MD to calculate the dielectric permittivity or viscosity. Examples that illustrate the use of these functionalities are given.

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Section: Journal Of Computational Chemistrysupporting

confidence: 85%

Section: Journal Of Computational Chemistrymentioning

confidence: 99%

Section: Journal Of Computational Chemistrymentioning

confidence: 99%

Section: Coarse-grained Supramolecular Force Field Termsmentioning

confidence: 99%

Section: Mixtures Of Coarse-grained Dmso or Meoh And Coarse-grained Wmentioning

confidence: 99%

See 3 more Smart Citations

New functionalities in the GROMOS biomolecular simulation software

Kunz¹,

Allison²,

Geerke³

et al. 2011

J Comput Chem

Self Cite

105

View full text Add to dashboard Cite

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Comparative Analysis of Protein Hydration from MD simulations with Additive and Polarizable Force Fields

Ngo

Fanning

Noskov

2018

Advcd Theory and Sims

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Recent development of the Drude polarizable (Drude) force field (FF), based on the extension of an induced dipole model, has reached a milestone in the past few years providing a complete set of polarizable parameters for proteins, water, ions, and many lipid types. This FF enables stable simulations up to microseconds, surpassing the capability of other polarizable FFs. The quality of the Drude FF, however, has remained largely untested for modeling the secondary structures of small peptides in explicit solvents compared with classical non-polarizable FFs. It is critical to benchmark the complex and mutually dependent dynamics of hydrogen-bond (H-bond) networks formed by water-water, protein-water, and protein-protein interactions that are expected to have a major impact on the stability of protein structures and their conformational space. Here, a direct comparison is presented between the current Drude FF and the CHARMM-36 non-polarizable classical FF for 1) the solvation free energy of mimetics for all amino acid side-chain equivalents, 2) limited conformational space, 3) protein-water and protein-protein interactions, and 4) the comparative lifetimes of H-bonds. The impact of counterions on the stabilization of secondary structure in model peptides is additionally discussed and compared between these FFs.

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A polarizable empirical force field for molecular dynamics simulation of liquid hydrocarbons

2014

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Electronic polarizability is usually treated implicitly in molecular simulations, which may lead to imprecise or even erroneous molecular behavior in spatially electronically inhomogeneous regions of systems such as proteins, membranes, interfaces between compounds, or mixtures of solvents. The majority of available molecular force fields and molecular dynamics simulation software packages does not account explicitly for electronic polarization. Even the simplest charge-on-spring (COS) models have only been developed for few types of molecules. In this work, we report a polarizable COS model for cyclohexane, as this molecule is a widely used solvent, and for linear alkanes, which are also used as solvents, and are the precursors of lipids, amino acid side chains, carbohydrates, or nucleic acid backbones. The model is an extension of a nonpolarizable united-atom model for alkanes that had been calibrated against experimental values of the density, the heat of vaporization and the Gibbs free energy of hydration for each alkane. The latter quantity was used to calibrate the parameters governing the interaction of the polarizable alkanes with water. Subsequently, the model was tested for other structural, thermodynamic, dielectric, and dynamic properties such as trans/gauche ratios, excess free energy, static dielectric permittivity, and self-diffusion. A good agreement with the experimental data for a large set of properties for each considered system was obtained, resulting in a transferable set of polarizable force-field parameters for CH2, CH3, and CH4 moieties.

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Development of a Nonlinear Classical Polarization Model for Liquid Water and Aqueous Solutions: COS/D

Cited by 82 publications

References 78 publications

New functionalities in the GROMOS biomolecular simulation software

New functionalities in the GROMOS biomolecular simulation software

Comparative Analysis of Protein Hydration from MD simulations with Additive and Polarizable Force Fields

A polarizable empirical force field for molecular dynamics simulation of liquid hydrocarbons

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