scholarly journals Molecular Dynamics Simulations of the Dynamic and Energetic Properties of Alkali and Halide Ions Using Water-Model-Specific Ion Parameters

2009 ◽  
Vol 113 (40) ◽  
pp. 13279-13290 ◽  
Author(s):  
In Suk Joung ◽  
Thomas E. Cheatham
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Water Model ◽  
Halide Ions ◽  
Energetic Properties ◽  
Dynamics Simulations

scholarly journals Thermodynamic Study of Hydrolysis Reactions in Aqueous Solution fromAb InitioPotential and Molecular Dynamics Simulations

2013 ◽  
Vol 2013 ◽  
pp. 1-8 ◽  
Author(s):  
S. Tolosa ◽  
A. Hidalgo ◽  
J. A. Sansón
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Free Energy ◽  
Reaction Mechanism ◽  
Molecular Dynamics Simulations ◽  
Infinite Dilution ◽  
Theoretical Study ◽  
Water Model ◽  
Dynamics Simulations ◽  
Hydrolysis Of

A procedure for the theoretical study of chemical reactions in solution by means of molecular dynamics simulations of aqueous solution at infinite dilution is described usingab initiosolute-solvent potentials and TIP3P water model to describe the interactions. The procedure is applied to the study of neutral hydrolysis of various molecules (HCONH2, HNCO, HCNHNH2, and HCOOCH3) via concerted and water-assisted mechanisms. We used the solvent as a reaction coordinate and the free energy curves for the calculation of the properties related with the reaction mechanism, namely, reaction and activation energies.

scholarly journals Accurate Simulations of Lipid Monolayers Require a Water Model With Correct Surface Tension

2021 ◽  
Author(s):  
Carmelo Tempra ◽  
O.H. Samuli Ollila ◽  
Matti Javanainen
Keyword(s):  
Molecular Dynamics ◽  
Surface Tension ◽  
Molecular Dynamics Simulations ◽  
Long Range ◽  
Van Der Waals ◽  
Water Model ◽  
Lipid Monolayers ◽  
Experimental Surface ◽  
Water Models ◽  
Dynamics Simulations

Lipid monolayers provide our lungs and eyes their functionality, and serve as proxy systems in biomembrane research. Therefore, lipid monolayers have been studied intensively also using molecular dynamics simulations, which are able to probe their lateral structure and interactions with, e.g., pharmaceuticals or nanoparticles. However, such simulations have struggled in describing the forces at the air–water interface. Particularly the surface tension of water and long-range van der Waals interactions have been considered critical, but their importance in monolayer simulations has been evaluated only separately. Here we combine the recent C36/LJ-PME lipid force field that in- cludes long-range van der Waals forces with water models that reproduce experimental surface tensions to elucidate the importance of these contributions in monolayer simulations. Our results suggest that a water model with correct surface tension is necessary to reproduce experimental surface pressure–area isotherms and monolayer phase behavior, while standard cutoff-based CHARMM36 lipid model with the 4-point OPC water model still provides the best agreement with experiments. Our results emphasize the importance of using high quality water models in applications and parameter development in molecular dynamics simulations of biomolecules.

scholarly journals Homogeneous nucleation of carbon dioxide in supersonic nozzles II: molecular dynamics simulations and properties of nucleating clusters

2021 ◽  
Author(s):  
Roope Halonen ◽  
Valtteri Tikkanen ◽  
Bernhard Reischl ◽  
Kayane K. Dingilian ◽  
Barbara E. Wyslouzil ◽  
...  
Keyword(s):  
Carbon Dioxide ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Gas Phase ◽  
Homogeneous Nucleation ◽  
Supersonic Nozzles ◽  
Energetic Properties ◽  
Dynamics Simulations ◽  
Carbon Dioxide Clusters

Molecular dynamics simulations reveal the structural and energetic properties of carbon dioxide clusters nucleating in the gas phase at extreme undercooling.

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