The shear viscosities of common water models by non-equilibrium molecular dynamics simulations

Song, Yanmei; Dai, Lenore L.

doi:10.1080/08927021003720553

Cited by 61 publications

(56 citation statements)

References 39 publications

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“…Both of them, small and large amplitude points, were discarded from the viscosity linear relationship adjustment. 116 From Fig. S3b, † it can be observed that acceleration amplitude values higher than a 0 ¼ 0.11 nm ps À2 do not deviate the temperature considerably from the dotted line, in this same gure only one standard deviation within each viscosity point was plotted.…”

Section: Shear Viscositiesmentioning

confidence: 82%

Thermodynamic, structural and dynamic properties of ionic liquids [C₄mim][CF₃COO], [C₄mim][Br] in the condensed phase, using molecular simulations

et al. 2019

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Section: Shear Viscositiesmentioning

confidence: 82%

Thermodynamic, structural and dynamic properties of ionic liquids [C₄mim][CF₃COO], [C₄mim][Br] in the condensed phase, using molecular simulations

et al. 2019

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“…2d ) to avoid steric clash with bound NCoR peptide. We ran simulations at 37 °C (NMR was run at 25 °C) and with the TIP3P water model (TIP3P is much less viscous than actual water 39 ) to speed relaxation to a local or global energy minimum (i.e., stable conformation) given that this chain B-inactive conformation may be in a higher energy conformation. These simulations were allowed to run until reaching a structure that remained reasonably stable for at least 5 μs as judged by consistent helix 12 RMSD relative to the starting structure (Supplementary Fig.…”

Section: Resultsmentioning

confidence: 99%

Defining a conformational ensemble that directs activation of PPARγ

Chrisman¹,

Nemetchek²,

Vera³

et al. 2018

Nat Commun

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The nuclear receptor ligand-binding domain (LBD) is a highly dynamic entity. Crystal structures have defined multiple low-energy LBD structural conformations of the activation function-2 (AF-2) co-regulator-binding surface, yet it remains unclear how ligand binding influences the number and population of conformations within the AF-2 structural ensemble. Here, we present a nuclear receptor co-regulator-binding surface structural ensemble in solution, viewed through the lens of fluorine-19 (19F) nuclear magnetic resonance (NMR) and molecular simulations, and the response of this ensemble to ligands, co-regulator peptides and heterodimerization. We correlate the composition of this ensemble with function in peroxisome proliferator-activated receptor-γ (PPARγ) utilizing ligands of diverse efficacy in co-regulator recruitment. While the co-regulator surface of apo PPARγ and partial-agonist-bound PPARγ is characterized by multiple thermodynamically accessible conformations, the full and inverse-agonist-bound PPARγ co-regulator surface is restricted to a few conformations which favor coactivator or corepressor binding, respectively.

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“…For example, Wensink et al 18 calculated the value of the viscosity for the TIP4P model at T = 298.25 K and found the values μ = 0.464 ± 0.003 mPa (48.2% error) and μ = 0.479 ± 0.009 mPa (46.5% error) using the periodic perturbation method. Song and Dai 19 used the same method and found the values μ = 0.505 ± 0.007 mPa (43.6% error) and 17 used the Stokes-Einstein relation and reported only errors, which are between 30.3% and 52.3% for experimental and calculated values. The reference simulation performed using the method described in this article leads to a value for the viscosity: μ = 0.481 ± 0.015 mPa (46.3% error) and therefore similar to the results obtained by others using different methods.…”

Section: B Viscosity Of the Water Modelsmentioning

confidence: 99%

A comparison of the value of viscosity for several water models using Poiseuille flow in a nano-channel

Markesteijn

Hartkamp

Luding

et al. 2012

The Journal of Chemical Physics

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The viscosity-temperature relation is determined for the water models SPC/E, TIP4P, TIP4P/Ew, and TIP4P/2005 by considering Poiseuille flow inside a nano-channel using molecular dynamics. The viscosity is determined by fitting the resulting velocity profile (away from the walls) to the continuum solution for a Newtonian fluid and then compared to experimental values. The results show that the TIP4P/2005 model gives the best prediction of the viscosity for the complete range of temperatures for liquid water, and thus it is the preferred water model of these considered here for simulations where the magnitude of viscosity is crucial. On the other hand, with the TIP4P model, the viscosity is severely underpredicted, and overall the model performed worst, whereas the SPC/E and TIP4P/Ew models perform moderately.

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The shear viscosities of common water models by non-equilibrium molecular dynamics simulations

Cited by 61 publications

References 39 publications

Thermodynamic, structural and dynamic properties of ionic liquids [C₄mim][CF₃COO], [C₄mim][Br] in the condensed phase, using molecular simulations

Thermodynamic, structural and dynamic properties of ionic liquids [C₄mim][CF₃COO], [C₄mim][Br] in the condensed phase, using molecular simulations

Defining a conformational ensemble that directs activation of PPARγ

A comparison of the value of viscosity for several water models using Poiseuille flow in a nano-channel

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The shear viscosities of common water models by non-equilibrium molecular dynamics simulations

Cited by 61 publications

References 39 publications

Thermodynamic, structural and dynamic properties of ionic liquids [C4mim][CF3COO], [C4mim][Br] in the condensed phase, using molecular simulations

Thermodynamic, structural and dynamic properties of ionic liquids [C4mim][CF3COO], [C4mim][Br] in the condensed phase, using molecular simulations

Defining a conformational ensemble that directs activation of PPARγ

A comparison of the value of viscosity for several water models using Poiseuille flow in a nano-channel

Contact Info

Product

Resources

About

Thermodynamic, structural and dynamic properties of ionic liquids [C₄mim][CF₃COO], [C₄mim][Br] in the condensed phase, using molecular simulations

Thermodynamic, structural and dynamic properties of ionic liquids [C₄mim][CF₃COO], [C₄mim][Br] in the condensed phase, using molecular simulations