scholarly journals On the transferability of ion parameters to the TIP4P/2005 water model using molecular dynamics simulations

2020 ◽  
Vol 152 (2) ◽  
pp. 024501 ◽  
Author(s):  
Max F. Döpke ◽  
Othonas A. Moultos ◽  
Remco Hartkamp
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Water Model ◽  
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.

QM/MM molecular dynamics simulations of the hydration of Mg(II) and Zn(II) ions

2013 ◽  
Vol 91 (7) ◽  
pp. 552-558 ◽  
Author(s):  
Saleh Riahi ◽  
Benoît Roux ◽  
Christopher N. Rowley
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Density Functional ◽  
Distribution Functions ◽  
Water Model ◽  
Polarizable Force Field ◽  
Water Solvent ◽  
Dynamics Simulations ◽  
Good Agreement

The hydration of Mg2+ and Zn2+ is examined using molecular dynamics simulations using 3 computational approaches of increasing complexity: the CHARMM nonpolarizable force field based on the TIP3P water model, the Drude polarizable force field based on the SWM4-NDP water model, and a combined QM/MM approach in which the inner coordination sphere is represented using a high-quality density functional theory (DFT) model (PBE/def2-TZVPP), and the remainder of the bulk water solvent is represented using the polarizable SWM4-NDP water model. The characteristic structural distribution functions (radial, angular, and tilt) are comparedand show very good agreement between the polarizable force field and QM/MM approaches. They predict an average Mg–O distance of 2.11 Å and an Zn–O distance of 2.13 Å, in good agreement with the available experimental neutron scattering and EXAFS data, while the Mg–O distances calculated using the nonpolarizable force field are 0.1 Å too short. Mg2+ (aq) and Zn2+ (aq) both have a coordination number of 6 and have a remarkably similar octahedral coordination mode, despite the chemical differences between these ions. Thermodynamic integration was used to calculate the relative hydration free energies of these ions (ΔΔGhydr). The nonpolarizable model is in error by 60 kcal mol– 1 and incorrectly predicts that Mg2+ has the more negative hydration energy. The Drude polarizable model predicts a ΔΔGhydr of only –13.2 kcal kcal mol– 1, an improvement over the results of the nonpolarizable force field, but still signficantly different than the experimental value of –30.1 kcal mol–1. The combined QM/MM approach performs much better, predicting a ΔΔGhydr of –34.8 kcal mol–1 in excellent agreement with experiment. These calculations support the experimental observation that Zn2+ has more favourable solvation free energy than Mg2+ despite having a very similar solvation structure.

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