A modified TIP3P water potential for simulation with Ewald summation

Abstract

The charges and Lennard-Jones parameters of the TIP3P water potential have been modified to improve its performance under the common condition for molecular dynamics simulations of using Ewald summation in lieu of relatively short nonbonded truncation schemes. These parameters were optimized under the condition that the hydrogen atoms do not have Lennard-Jones parameters, thus making the model independent of the combining rules used for the calculation of nonbonded, heteroatomic interaction energies, and limiting the number of Lennard-Jones calculations required. Under these conditions, this model provides accurate density (rho = 0.997 g/ml) and heat of vaporization (DeltaH(vap) = 10.53 kcal/mol) at 25 degrees C and 1 atm, but also provides improved structure in the second peak of the O-O radial distribution function and improved values for the dielectric constant (epsilon(0) = 89) and the diffusion coefficient (D = 4.0 x 10(-5) cm(2)/s) relative to the original parametrization. Like the original parameterization, however, this model does not show a temperature density maximum. Several similar models are considered with the additional constraint of trying to match the performance of the optimized potentials for liquid simulation atom force field to that obtained when using the simulation conditions under which it was originally designed, but no model was entirely satisfactory in reproducing the relative difference in free energies of hydration between the model compounds, phenol and benzene. Finally, a model that incorporates a long-range correction for truncated Lennard-Jones interactions is presented, which provides a very accurate dielectric constant (epsilon(0) = 76), however, the improvement in this estimate is on the same order as the uncertainty in the calculation.

Evaluation of various water models for simulation of adsorption in hydrophobic zeolites

“…As polarity is more important than polarisability in the adsorption of molecules in these materials, in our study, we select the non-polarisable Tip5pEw [42] model for water, which is simply a Tip5p model parameterised for Ewald sums. Similar models such as Tip4pEw [43], Tip3p-PME [44], SPC/Fw [45] or SWM4-DP [46] are also possible candidates, though some of them are flexible or polarisable and they might give a better description of some particular properties of the system at a larger computational cost. The SPC, Tip4p and other similar models can also be used in the study of water adsorption in zeolites, but due to the importance of the long-range interactions, their Ewald-fitted versions should be used instead.…”

“…The model Tip5pEw [42] is a suitable model for studying adsorption of water in zeolites, because its properties have been refitted using Ewald sums and the adsorption isotherms can be computed with a good precision. There are other models that also have been parameterised with Ewald sums, such as Tip4pEw [43], Tip3p-PME [44], SPC/Fw [45] molecular dynamics (MD) or SWM4-DP [46]. The last two are flexible water models and therefore their use would increase the simulation time.…”

Solvent reaction field potential inside an uncharged globular protein: A bridge between implicit and explicit solvent models?

“…In particular, restricting the negative charge on the water molecule to travel strictly with the Lennard-Jones site may create adverse effects at the water-protein interface in addition to the compromises that must be made to achieve certain properties of water under a biologically relevant set of conditions [86]. Price and Brooks [87] noted that three-point models, used in the vast majority of explicitsolvent molecular dynamics simulations, may be unable to achieve the dipole moment of water in solution (which has been observed experimentally to be as high as 2.9 D, or 0.60 e c Å −1 [36]) in conjunction with a realistic dielectric constant, density, and thermodynamic properties. Additional problems related to the dipole moment arise from the rigid nature of most water models, which in the present study permitted vastly accelerated sampling with a 4 fs timestep.…”

The thermodynamic and ground state properties of the TIP4P water octamer

“…For example, the MCY ͑Matsuoka Clementi Yoshimine͒ potential 25 is among the earliest models derived by fitting a number of configuration interaction computations on the dimer. A number of empirical or semiempirical potentials are obtained by fitting experimental and simulated properties of liquid water [44][45][46][47][48][49][50][51] or ice. 52,53 In the present work, we focus on the water octamer for two main reasons.…”