Towards a dissociative SPC-like water model II. The impact of Lennard-Jones and Buckingham non-coulombic forces

Abstract

The dissociative water potential by Garofalini and coworkers has been re-formulated in the framework of the widely employed Lennard-Jones and Buckingham potentials, enhancing the transferability of the model to third party simulation programs.

Modelling bulk and surface characteristics of cubic CeO2, Gd2O3, and gadolinium-doped ceria using a partial charge framework

“…The newly developed potential presented in the work was shown to successfully describe the crystal structure of CeO 2 and Gd 2 O 3 at ambient conditions and elevated temperatures. The benefit of using partial charges is that the model can be used in conjunction with existing partial charge models such as a reactive water model developed earlier by Wiedemair 28,29 as well as force fields aimed at the description of organic and biomolecular systems. 58,59 This would enable simulations of surface processes such as the formation of a Helmholtz double layer and associated reactive corrosion process as well as the adsorption of organic molecules at GDC interfaces in the presence of liquid water.…”

“…The main objective of the parametrization is to ensure compatibility between the novel derived solid-state potentials and the reactive water model. 28,29 The latter explicitly accounts for proton transfer reactions. Therefore, it is not possible to apply various atom types per element.…”

A DFTB/MM MD Approach for Solid-State Interfaces: Structural and Dynamical Properties of H2O and NH3on R-TiO2(001)

“…The advantage of executing a DFTB-based equilibration over standard force-field approaches is linked to the fact that the formation and cleavage of chemical bonds as required to describe proton-transfer reactions are inherently accounted for in DFTB approaches. Although a number of dissociative/reactive force fields for the treatment of aqueous solutions are available in the literature, − ,− ,− potential parameters to describe the surface–water interactions have to be provided, which are even more difficult in their construction/balancing compared to nondissociative MM formulations. Because dissociative force fields are typically benchmarked against QM-based simulation results, the outlined QM/MM strategy (at both DFTB and DFT levels) may provide key reference data to verify reactive force fields aimed at the description of proton-transfer reactions near solid-state interfaces.…”

Pyruvate kinase deficiency and PKLR gene mutations: Insights from molecular dynamics simulation analysis

“…We performed MD simulations for the WT, R498H, and P366Lfs*12 proteins using the GROMACS [ 19 ]. MD simulations were performed under constant temperature and pressure, as well as periodic boundary conditions, using the Amber14SB all-atom force field and transferable intermolecular potential 3 points water model [ 20 ]. The LINCS algorithm was employed to constrain all the bonds associated with hydrogen atoms, and the time step was set to 2 fs [ 20 ].…”