Validation and application of orientational order-based TMD prediction

Through our recent examination of four famous water models, we hypothesized that there should be common features of orientational order universally at the temperature for maximum density (TMD) of 1 g/cm³ whatever reasonable water model used. However, it was derived empirically rather than theoretically and it demands more severe tests eagerly to be a common law. In the present work, we tested two additional water models, TIP4P-2005 and TIP5P-Ew models developed recently. From this, we found the consistent common features of orientational order around reported values of TMD again. To demonstrate simple yet effective predictability of an unknown TMD for a certain water model using the method derived from our hypothesis, simulations of our method were carried out at several temperatures with intervals of 20 °C for TIP4P-ice model. In spite of its much less computational cost and temperature range that was chosen arbitrarily, TMD was predicted correctly with resolution of 20 °C at least. We propose that our method offers a useful guideline for TMD by narrowing down the choice of TMD candidates without heavy computational efforts, at least for point-charge water models.     

Dynamics of TIP5P and TIP4P/ice potentials

The dynamics of a thin film of ice Ih deposited on MgO (001) is studied through molecular dynamics simulations performed with two new potential models of ice. This system is chosen because it is possible to compare the results of the simulations to incoherent neutron quasielastic scattering experiments performed few years ago and to previous molecular dynamics simulations using the TIP4P potential model. The present simulations are performed to determine the evolution of the translational and orientational order parameters of the ice film upon temperature increase in the 250-280 K range. They are also used to calculate the translational and orientational diffusion coefficients of the water molecules in the supported film as a function of the temperature. When using the TIP5P potential, the present results show a better agreement with experimental data than those calculated with the TIP4P potential, especially regarding the temperature above which significant changes are obtained in the dynamics of the water film. Similar conclusions are obtained when using the TIP4P/ice potential, although this latter potential clearly underestimates the translational diffusion coefficients.     

Relation between the melting temperature and the temperature of maximum density for the most common models of water

Water exhibits a maximum in density at normal pressure at 4 degrees above its melting point. The reproduction of this maximum is a stringent test for potential models used commonly in simulations of water. The relation between the melting temperature and the temperature of maximum density for these potential models is unknown mainly due to our ignorance about the melting temperature of these models. Recently we have determined the melting temperature of ice I(h) for several commonly used models of water (SPC, SPC/E, TIP3P, TIP4P, TIP4P/Ew, and TIP5P). In this work we locate the temperature of maximum density for these models. In this way the relative location of the temperature of maximum density with respect to the melting temperature is established. For SPC, SPC/E, TIP3P, TIP4P, and TIP4P/Ew the maximum in density occurs at about 21-37 K above the melting temperature. In all these models the negative charge is located either on the oxygen itself or on a point along the H-O-H bisector. For the TIP5P and TIP5P-E models the maximum in density occurs at about 11 K above the melting temperature. The location of the negative charge appears as a geometrical crucial factor to the relative position of the temperature of maximum density with respect to the melting temperature.     

Liquid-liquid phase transitions in supercooled water studied by computer simulations of various water models

Liquid-liquid and liquid-vapor coexistence regions of various water models were determined by Monte Carlo (MC) simulations of isotherms of density fluctuation-restricted systems and by Gibbs ensemble MC simulations. All studied water models show multiple liquid-liquid phase transitions in the supercooled region: we observe two transitions of the TIP4P, TIP5P, and SPCE models and three transitions of the ST2 model. The location of these phase transitions with respect to the liquid-vapor coexistence curve and the glass temperature is highly sensitive to the water model and its implementation. We suggest that the apparent thermodynamic singularity of real liquid water in the supercooled region at about 228 K is caused by an approach to the spinodal of the first (lowest density) liquid-liquid phase transition. The well-known density maximum of liquid water at 277 K is related to the second liquid-liquid phase transition, which is located at positive pressures with a critical point close to the maximum. A possible order parameter and the universality class of liquid-liquid phase transitions in one-component fluids are discussed.     

Computer simulation of two new solid phases of water: Ice XIII and ice XIV

NpT Monte Carlo simulations have been performed for two recently discovered solid phases of water which have been denoted as ice XIII and ice XIV C. G. Salzmann et al. [Science311, 1758 (2006)]. Several potential models of water were considered, namely, the traditional SPC/E, TIP4P, and TIP5P and the more recent TIP5P-E, TIP4P-Ew, TIP4P/Ice, and TIP4P/2005 models. Significant differences in density and oxygen-oxygen radial distribution functions are found between the predictions of the SPC/E, TIP5P, and the models of the TIP4P family. The models TIP4P/Ice and TIP4P/2005 provide the best estimates of the density.     

Molecular dynamics simulations of the mechanisms of thermal conduction in methane hydrates

The thermal conductivity of methane hydrate is an important physical parameter affecting the processes of methane hydrate exploration,mining,gas hydrate storage and transportation as well as other applications.Equilibrium molecular dynamics simulations and the Green-Kubo method have been employed for systems from fully occupied to vacant occupied sI methane hydrate in order to estimate their thermal conductivity.The estimations were carried out at temperatures from 203.15 to 263.15 K and at pressures from 3 to 100 MPa.Potential models selected for water were TIP4P,TIP4P-Ew,TIP4P/2005,TIP4P-FQ and TIP4P/Ice.The effects of varying the ratio of the host and guest molecules and the external thermobaric conditions on the thermal conductivity of methane hydrate were studied.The results indicated that the thermal conductivity of methane hydrate is essentially determined by the cage framework which constitutes the hydrate lattice and the cage framework has only slightly higher thermal conductivity in the presence of the guest molecules.Inclusion of more guest molecules in the cage improves the thermal conductivity of methane hydrate.It is also revealed that the thermal conductivity of the sI hydrate shows a similar variation with temperature.Pressure also has an effect on the thermal conductivity,particularly at higher pressures.As the pressure increases,slightly higher thermal conductivities result.Changes in density have little impact on the thermal conductivity of methane hydrate.     

Benchmarking the thermodynamic analysis of water molecules around a model beta sheet

Water molecules play a vital role in biological and engineered systems by controlling intermolecular interactions in the aqueous phase. Inhomogeneous fluid solvation theory provides a method to quantify solvent thermodynamics from molecular dynamics or Monte Carlo simulations and provides an insight into intermolecular interactions. In this study, simulations of TIP4P‐2005 and TIP5P‐Ewald water molecules around a model beta sheet are used to investigate the orientational correlations and predicted thermodynamic properties of water molecules at a protein surface. This allows the method to be benchmarked and provides information about the effect of a protein on the thermodynamics of nearby water molecules. The results show that the enthalpy converges with relatively little sampling, but the entropy and thus the free energy require considerably more sampling to converge. The two water models yield a very similar pattern of hydration sites, and these hydration sites have very similar thermodynamic properties, despite notable differences in their orientational preferences. The results also predict that a protein surface affects the free energy of water molecules to a distance of approximately 4.0 Å, which is in line with previous work. In addition, all hydration sites have a favorable free energy with respect to bulk water, but only when the water–water entropy term is included. A new technique for calculating this term is presented and its use is expected to be very important in accurately calculating solvent thermodynamics for quantitative application. © 2012 Wiley Periodicals, Inc.     

The melting temperature of the most common models of water

The melting temperature of ice I(h) for several commonly used models of water (SPC, SPC/E,TIP3P,TIP4P, TIP4P/Ew, and TIP5P) is obtained from computer simulations at p = 1 bar. Since the melting temperature of ice I(h) for the TIP4P model is now known [E. Sanz, C. Vega, J. L. F. Abascal, and L. G. MacDowell, Phys. Rev. Lett. 92, 255701 (2004)], it is possible to use the Gibbs-Duhem methodology [D. Kofke, J. Chem. Phys. 98, 4149 (1993)] to evaluate the melting temperature of ice I(h) for other potential models of water. We have found that the melting temperatures of ice I(h) for SPC, SPC/E, TIP3P, TIP4P, TIP4P/Ew, and TIP5P models are T = 190 K, 215 K, 146 K, 232 K, 245 K, and 274 K, respectively. The relative stability of ice I(h) with respect to ice II for these models has also been considered. It turns out that for SPC, SPC/E, TIP3P, and TIP5P the stable phase at the normal melting point is ice II (so that ice I(h) is not a thermodynamically stable phase for these models). For TIP4P and TIP4P/Ew, ice I(h) is the stable solid phase at the standard melting point. The location of the negative charge along the H-O-H bisector appears as a critical factor in the determination of the relative stability between the I(h) and II ice forms. The methodology proposed in this paper can be used to investigate the effect upon a coexistence line due to a change in the potential parameters.     

Characterization of the TIP4P-Ew water model: vapor pressure and boiling point

The liquid-vapor-phase equilibrium properties of the previously developed TIP4P-Ew water model have been studied using thermodynamic integration free-energy simulation techniques in the temperature range of 274-400 K. We stress that free-energy results from simulations need to be corrected in order to be compared to the experiment. This is due to the fact that the thermodynamic end states accessible through simulations correspond to fictitious substances (classical rigid liquids and classical rigid ideal gases) while experiments operate on real substances (liquids and real gases, with quantum effects). After applying analytical corrections the vapor pressure curve obtained from simulated free-energy changes is in excellent agreement with the experimental vapor pressure curve. The boiling point of TIP4P-Ew water under ambient pressure is found to be at 370.3+/-1.9 K, about 7 K higher than the boiling point of TIP4P water (363.7+/-5.1 K; from simulations that employ finite range treatment of electrostatic and Lennard-Jones interactions). This is in contrast to the approximately +15 K by which the temperature of the density maximum and the melting temperature of TIP4P-Ew are shifted relative to TIP4P, indicating that the temperature range over which the liquid phase of TIP4P-Ew is stable is narrower than that of TIP4P and resembles more that of real water. The quality of the vapor pressure results highlights the success of TIP4P-Ew in describing the energetic and entropic aspects of intermolecular interactions in liquid water.     

Performance of the general amber force field in modeling aqueous POPC membrane bilayers

The aim of this work was to answer the question of whether the general amber force field (GAFF) is good enough to simulate fully hydrated POPC membrane bilayers. The test system contained 128 POPC and 2985 TIP3P water molecules. The equilibration was carried out in a nonarbitrary manner to reach the stable liquid-crystalline phase. The simulations were performed by using particle mesh Ewald electrostatics implemented in molecular dynamics packages Amber8 (NPT ensembles) and NAMD2 (NPgammaT ensembles). The computational results were assessed against the following experimental membrane properties: (i) area per lipid, (ii) area compressibility modulus, (iii) order parameter, (iv) gauche conformations per acyl chain, (v) lateral diffusion coefficients, (vi) electron density profile, and (vii) bound water at the lipid/water interface. The analyses revealed that the tested force field combination approximates the experimental values at an unexpectedly good level when the NPgammaT ensemble is applied with a surface tension of 60 mN m(-1) per bilayer. It is concluded that the GAFF/TIP3P combination can be utilized for aqueous membrane bilayer simulations, as it provides acceptable accuracy for biomolecular modeling.     

The melting point of ice Ih for common water models calculated from direct coexistence of the solid-liquid interface

In this work we present an implementation for the calculation of the melting point of ice I(h) from direct coexistence of the solid-liquid interface. We use molecular dynamics simulations of boxes containing liquid water and ice in contact. The implementation is based on the analysis of the evolution of the total energy along NpT simulations at different temperatures. We report the calculation of the melting point of ice I(h) at 1 bar for seven water models: SPC/E, TIP4P, TIP4P-Ew, TIP4P/ice, TIP4P/2005, TIP5P, and TIP5P-E. The results for the melting temperature from the direct coexistence simulations of this work are in agreement (within the statistical uncertainty) with those obtained previously by us from free energy calculations. By taking into account the results of this work and those of our free energy calculations, recommended values of the melting point of ice I(h) at 1 bar for the above mentioned water models are provided.     

An empirical boundary potential for water droplet simulations

An empirical modified boundary potential has been derived to correct the structural perturbations arising from the presence of the vacuum boundary in the simulation of spherical TIP4P water systems. The potential is parameterized for a 12.0-Å sphere of TIP4P water and gives improved number density and orientational sampling behavior. It is also transferable to both larger and smaller simulation systems with only a moderate degradation in performance. Free-energy calculations have been conducted for the perturbation of a TIP4P water molecule to methane under aqueous conditions, and the modified boundary potential gives results consistent with those from simulations using periodic boundary conditions. However, simple half-harmonic boundary potentials give unsatisfactory number density, orientational sampling, and free-energy results. Moreover, use of the modified boundary potential results in a negligible increase in simulation time. It is envisaged that the modified boundary potential will find use in free-energy perturbation calculations on proteins with a solvent sphere centered on the active site. © 1995 by John Wiley & Sons, Inc.     

The thickness of a liquid layer on the free surface of ice as obtained from computer simulation

Molecular dynamic simulations were performed for ice I(h) with a free surface by using four water models, SPC/E, TIP4P, TIP4P/Ice, and TIP4P/2005. The behavior of the basal plane, the primary prismatic plane, and of the secondary prismatic plane when exposed to vacuum was analyzed. We observe the formation of a thin liquid layer at the ice surface at temperatures below the melting point for all models and the three planes considered. For a given plane it was found that the thickness of a liquid layer was similar for different water models, when the comparison is made at the same undercooling with respect to the melting point of the model. The liquid layer thickness is found to increase with temperature. For a fixed temperature it was found that the thickness of the liquid layer decreases in the following order: the basal plane, the primary prismatic plane, and the secondary prismatic plane. For the TIP4P/Ice model, a model reproducing the experimental value of the melting temperature of ice, the first clear indication of the formation of a liquid layer, appears at about -100 degrees C for the basal plane, at about -80 degrees C for the primary prismatic plane, and at about -70 degrees C for the secondary prismatic plane.     

Molecular dynamics simulations of vapor/liquid coexistence using the nonpolarizable water models

The surface tension, vapor-liquid equilibrium densities, and equilibrium pressure for common water models were calculated using molecular dynamics simulations over temperatures ranging from the melting to the critical points. The TIP4P/2005 and TIP4P-i models produced better values for the surface tension than the other water models. We also examined the correlation of the data to scaling temperatures based on the critical and melting temperatures. The reduced temperature (T/T(c)) gives consistent equilibrium densities and pressure, and the shifted temperature T + (T(c, exp) - T(c, sim)) gives consistent surface tension among all models considered in this study. The modified fixed charge model which has the same Lennard-Jones parameters as the TIP4P-FQ model but uses an adjustable molecular dipole moment is also simulated to find the differences in the vapor-liquid coexistence properties between fixed and fluctuating charge models. The TIP4P-FQ model (2.72 Debye) gives the best estimate of the experimental surface tension. The equilibrium vapor density and pressure are unaffected by changes in the dipole moment as well as the surface tension and liquid density.     

Capillary waves at the liquid-vapor interface and the surface tension of water

Capillary waves occurring at the liquid-vapor interface of water are studied using molecular dynamics simulations. In addition, the surface tension, determined thermodynamically from the difference in the normal and tangential pressure at the liquid-vapor interface, is compared for a number of standard three- and four-point water models. We study four three-point models (SPC/E, TIP3P, TIP3P-CHARMM, and TIP3P-Ew) and two four-point models (TIP4P and TIP4P-Ew). All of the models examined underestimate the surface tension; the TIP4P-Ew model comes closest to reproducing the experimental data. The surface tension can also be determined from the amplitude of capillary waves at the liquid-vapor interface by varying the surface area of the interface. The surface tensions determined from the amplitude of the logarithmic divergence of the capillary interfacial width and from the traditional thermodynamic method agree only if the density profile is fitted to an error function instead of a hyperbolic tangent function.     

A comparison of the value of viscosity for several water models using Poiseuille flow in a nano-channel

The viscosity-temperature relation is determined for the water models SPC/E, TIP4P, TIP4P/Ew, and TIP4P/2005 by considering Poiseuille flow inside a nano-channel using molecular dynamics. The viscosity is determined by fitting the resulting velocity profile (away from the walls) to the continuum solution for a Newtonian fluid and then compared to experimental values. The results show that the TIP4P/2005 model gives the best prediction of the viscosity for the complete range of temperatures for liquid water, and thus it is the preferred water model of these considered here for simulations where the magnitude of viscosity is crucial. On the other hand, with the TIP4P model, the viscosity is severely underpredicted, and overall the model performed worst, whereas the SPC/E and TIP4P/Ew models perform moderately.