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Optimized Magnesium Force Field Parameters for Biomolecular Simulations with Accurate Solvation, Ion-Binding, and Water-Exchange Properties in SPC/E, TIP3P-fb, TIP4P/2005, TIP4P-Ew, and TIP4P-D.

ABSTRACT: Magnesium is essential in many vital processes. To correctly describe Mg²⁺ in physiological processes by molecular dynamics simulations, accurate force fields are fundamental. Despite the importance, force fields based on the commonly used 12-6 Lennard-Jones potential showed significant shortcomings. Recently progress was made by an optimization procedure that implicitly accounts for polarizability. The resulting microMg and nanoMg force fields (J. Chem. Theory Comput. 2021, 17, 2530-2540) accurately reproduce a broad range of experimental solution properties and the binding affinity to nucleic acids in TIP3P water. Since countless simulation studies rely on available water models and ion force fields, we here extend the optimization and provide Mg²⁺ parameters in combination with the SPC/E, TIP3P-fb, TIP4P/2005, TIP4P-Ew, and TIP4P-D water models. For each water model, the Mg²⁺ force fields reproduce the solvation free energy, the distance to oxygens in the first hydration shell, the hydration number, the activity coefficient derivative in MgCl₂ solutions, and the binding affinity and distance to the phosphate oxygens on nucleic acids. We present two parameter sets: MicroMg yields water exchange on the microsecond time scale and matches the experimental exchange rate. Depending on the water model, nanoMg yields accelerated water exchange in the range of 10⁶ to 10⁸ exchanges per second. The nanoMg parameters can be used to enhance the sampling of binding events, to obtain converged distributions of Mg²⁺, or to predict ion binding sites in biomolecular simulations. The parameter files are freely available at https://github.com/bio-phys/optimizedMgFFs.

SUBMITTER: Grotz KK

PROVIDER: S-EPMC8757469 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Divalent metal ions play important roles in biological and materials systems. Molecular dynamics simulation is an efficient tool to investigate these systems at the microscopic level. Recently, four new water models (OPC3, OPC, TIP3P-FB, and TIP4P-FB) have been developed and better represent the physical properties of water than previous models. Metal ion parameters are dependent on the water model employed, making it necessary to develop metal ion parameters for select new water models. In the present work, we performed parameter scanning for the 12-6 Lennard-Jones nonbonded model of divalent metal ions in conjunction with the four new water models as well as four previous water models (TIP3P, SPC/E, TIP4P, and TIP4P-Ew). We found that these new three-point and four-point water models provide comparable or significantly improved performance for the simulation of divalent metal ions when compared to previous water models in the same category. Among all eight water models, the OPC3 water model yields the best performance for the simulation of divalent metal ions in the aqueous phase when using the 12-6 model. On the basis of the scanning results, we independently parametrized the 12-6 model for 24 divalent metal ions with each of the four new water models. As noted previously, the 12-6 model still fails to simultaneously reproduce the experimental hydration free energy (HFE) and ion-oxygen distance (IOD) values even with these new water models. To solve this problem, we parametrized the 12-6-4 model for the 16 divalent metal ions for which we have both experimental HFE and IOD values for each of the four new water models. The final parameters are able to reproduce both the experimental HFE and IOD values accurately. To validate the transferability of our parameters, we carried out benchmark calculations to predict the energies and geometries of ion-water clusters as well as the ion diffusivity coefficient of Mg2+. By comparison to quantum chemical calculations and experimental data, these results show that our parameters are well designed and have excellent transferability. The metal ion parameters for the 12-6 and 12-6-4 models reported herein can be employed in simulations of various biological and materials systems when using the OPC3, OPC, TIP3P-FB, or TIP4P-FB water model.

Dataset Information

Optimized Magnesium Force Field Parameters for Biomolecular Simulations with Accurate Solvation, Ion-Binding, and Water-Exchange Properties in SPC/E, TIP3P-fb, TIP4P/2005, TIP4P-Ew, and TIP4P-D.

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