Accurate Water Models Research Articles

Molecular Dynamics Simulations of Proteins: Can the Explicit Water Model Be Varied?

In molecular mechanics simulations of biological systems, the solvation water is typically represented by a default water model which is an integral part of the force field. Indeed, protein nonbonding parameters are chosen in order to obtain a balance between water-water and protein-water interactions and hence a reliable description of protein solvation. However, less attention has been paid to the question of whether the water model provides a reliable description of the water properties under the chosen simulation conditions, for which more accurate water models often exist. Here we consider the case of the CHARMM protein force field, which was parametrized for use with a modified TIP3P model. Using quantum mechanical and molecular mechanical calculations, we investigate whether the CHARMM force field can be used with other water models: TIP4P and TIP5P. Solvation properties of N-methylacetamide (NMA), other small solute molecules, and a small protein are examined. The results indicate differences in binding energies and minimum energy geometries, especially for TIP5P, but the overall description of solvation is found to be similar for all models tested. The results provide an indication that molecular mechanics simulations with the CHARMM force field can be performed with water models other than TIP3P, thus enabling an improved description of the solvent water properties.

Metastable liquid-liquid coexistence and density anomalies in a core-softened fluid

Linearly sloped or "ramp" potentials belong to a class of core-softened models which possess a liquid-liquid critical point (LLCP) in addition to the usual liquid-gas critical point. Furthermore, they exhibit thermodynamic anomalies in their density and compressibility, the nature of which may be akin to those occurring in water. Previous simulation studies of ramp potentials have focused on just one functional form, for which the LLCP is thermodynamically stable. In this work we construct a series of ramp potentials, which interpolate between this previously studied form and a ramp-based approximation to the Lennard-Jones (LJ) potential. By means of Monte Carlo simulation, we locate the LLCP, the first order high density liquid (HDL)-low density liquid (LDL) coexistence line, and the line of density maxima for a selection of potentials in the series. We observe that as the LJ limit is approached, the LLCP becomes metastable with respect to freezing into a hexagonal close packed crystalline solid. The qualitative nature of the phase behavior in this regime shows a remarkable resemblance to that seen in simulation studies of accurate water models. Specifically, the density of the liquid phase exceeds that of the solid; the gradient of the metastable LDL-HDL line is negative in the pressure (p)-temperature (T) plane; while the line of density maxima in the p-T plane has a shape similar to that seen in water and extends into the stable liquid region of the phase diagram. As such, our results lend weight to the "second critical point" hypothesis as an explanation for the anomalous behavior of water.