Natural organic matter (NOM) represents a complex molecular system that cannot be fully characterized compositionally or structurally in full atomistic detail. This makes the application of molecular modeling approaches very difficult and significantly hinders quantitative investigation of NOM properties and behavior by these otherwise very efficient computational techniques. Here we report and analyze three molecular dynamics (MD) simulations of Ca2+ complexation with NOM in aqueous solutions in an attempt to quantitatively assess possible effects of model- and system size-dependence in such simulations. Despite some obvious variations in the computed results that depend on the size of the simulated system and on the parameters of the force field models used, all three simulations are quite robust and consistent. They show Ca2+ ions associated with 35-50% of the NOM carboxylic groups at near-neutral pH and point to a strong preference for the stability of bidentate-coordinated contact ion pairs. The degree and potential mechanisms of NOM supramolecular aggregation in the presence of Ca2+ ions in solution are also assessed on a semi-quantitative level from two larger-scale MD simulations.