Accuracy of TIP4P/2005 and SPC/Fw Water Models

Abstract

Water is used as the main solvent in model systems containing bioorganic molecules. Choosing the right water model is an important step in the study of the biophysical and biochemical processes that occur in cells. In the present work, we perform molecular dynamics simulations using two distinct force fields for water: the rigid model TIP4P/2005, where only intermolecular interactions are considered, and the flexible model SPC/Fw, where intramolecular interactions are also taken into account. The simulations aim to determine the effect of the inclusion of intramolecular interactions on the accuracy of calculated properties of bulk water (density and thermal expansion coefficient, selfdiffusion coefficients, shear viscosity, radial distribution functions, and dielectric constant), as compared to experimental results, over a temperature range between 250 and 370 K. We find that the results of the rigid model present the smallest deviations relative to experiments for most of the calculated quantities, except for the shear viscosity of supercooled water and the water dielectric constant, where the flexible model presents better agreement with experiments.

Sequence and structural analysis of adaptors of Toll-like receptor 4 sheds light on the evolutionary trajectory and functional emergence

“…The system builder option was then used to prepare the system. TIP4P explicit solvent model was chosen, and a orthorhombic box was defined with minimum volume size [50]. The OPLS4 force field was selected and the whole system was neutralized by adding equivalent number of ions [51].…”