Multisite Ion Models That Improve Coordination and
Free Energy Calculations in Molecular Dynamics Simulations
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Abstract
Current
ion models in molecular mechanics are simple spheres, and their interactions
are solely determined from the van der Waals radius of the sphere
and the total charge. Here, we introduce a model where we distribute
the total charge of the ion into <i>n</i>-dummy centers
that are placed in the direction of the coordinating atoms. We have
parametrized this model for two divalent cations, Ca<sup>2+</sup> and
Mg<sup>2+</sup>, and have tested the model’s accuracy in a
variety of simulations. With this model we are not only able to correctly
predict the free energies and selectivity for cation binding sites
in proteins and nucleic acids, but we achieve better coordination
geometries and can capture more subtle effects such as the exchange
of inner shell waters. Additionally, this model does not employ higher-order
electrostatics and thus can be easily used with standard force fields