4313214

Parametrization of SWM4-HLJ and SMW3-NDP water models for the polarizable Drude oscillator force field

Date
August 19, 2025

Molecular dynamics (MD) simulations are widely used to investigate biological events attributed to its high spatial and temporal resolution that cannot be readily achieved by experiments. However, the accuracy relies greatly on the force field. The polarizable force fields based on the classical Drude oscillator model now includes the full range of biological macromolecules. While it has been shown to accurately model many systems, limitations are present including contributions due to the inaccuracy of the water model. Recently, we proposed 2 new water models, SWM4-HLJ and SWM3-NDP. Compared to its predecessor, SWM4-HLJ improves in many aspects, including density-temperature dependence, diffusion coefficient, viscosity, and microscopic water network interactions. All these make more accurate MD simulations possible. The efficient water model, SWM3-NDP, can speed up the MD simulations by ~30%, while maintaining the bulk phase properties at the ambient condition with some sacrifice in the zero-field dipole moment and density-temperature dependence.

The compatibility of the new water models with other important molecules in the Drude system was tested. Proteins and nucleic acids conformational properties are maintained. Most of the ions show better hydration free energies and stability of the simulations is improved, while only the interaction between the new water models and Mg2+ was further adjusted. With lipids, specific pairwise interactions were adjusted based on the hydration free energies and radial distribution functions of several model compounds yielding surface areas/head group and order parameters of lipids in good agreement with experiment. In conclusion, the new water models are compatible with the polarizable Drude biomolecular force field.

Presenter

Co-Authors

Speaker Image for Yiling Nan
Ph.D. Student, University of Alberta
Speaker Image for Alexander Mackerell
Univ. of Maryland, Pharmacy

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