United polarizable multipole water model for molecular mechanics simulation

Abstract

We report the development of a united AMOEBA (uAMOEBA) polarizable water model, which is computationally 3-5 times more efficient than the three-site AMOEBA03 model in molecular dynamics simulations while providing comparable accuracy for gas-phase and liquid properties. In this coarse-grained polarizable water model, both electrostatic (permanent and induced) and van der Waals representations have been reduced to a single site located at the oxygen atom. The permanent charge distribution is described via the molecular dipole and quadrupole moments and the many-body polarization via an isotropic molecular polarizability, all located at the oxygen center. Similarly, a single van der Waals interaction site is used for each water molecule. Hydrogen atoms are retained only for the purpose of defining local frames for the molecular multipole moments and intramolecular vibrational modes. The parameters have been derived based on a combination of ab initio quantum mechanical and experimental data set containing gas-phase cluster structures and energies, and liquid thermodynamic properties. For validation, additional properties including dimer interaction energy, liquid structures, self-diffusion coefficient, and shear viscosity have been evaluated. The results demonstrate good transferability from the gas to the liquid phase over a wide range of temperatures, and from nonpolar to polar environments, due to the presence of molecular polarizability. The water coordination, hydrogen-bonding structure, and dynamic properties given by uAMOEBA are similar to those derived from the all-atom AMOEBA03 model and experiments. Thus, the current model is an accurate and efficient alternative for modeling water. C 2015 AIP Publishing LLC. [http://dx

Water in Nanopores and Biological Channels: A Molecular Simulation Perspective

“… 105 A “coarse-grained” variant of the AMOEBA family, uAMOEBA, contains only polarizable sites on the oxygen centers, thereby producing a 3- to 5-fold computational acceleration with respect to the AMOEBA03 model. 106 Most recently, the aniso-AMOEBA water model has been developed to incorporate the effect of anisotropic polarizability. 107 A further variant on the induced dipole water model, GPCM, has been developed, which models the charges as Gaussian functions.…”

Self-diffusion coefficient of bulk and confined water: a critical review of classical molecular simulation studies

“…In the case of HBP, a short-ranged directional hydrogen-bonding interaction term is part of the potential and therefore water structure is also captured accurately. [158], uAMOEBA [367] and TL6P sk [172]. Although the diffusivity predictions of the models presented in Figure 3 (b) are not corrected for finite size effects, the use of at least 1,000 molecules is expected to yield a relatively good prediction (possibly within 10-15%, depending on the accuracy in the computed viscosity) and therefore some force fields of the IPOL-and COS/-families are expected to be close to the experimental value.…”

“…Wang et al [167] reports D for AMOEBA to be equal to 2.0 x 10 -9 m 2 /s which has a relative deviation from the experimental value equal to -13%. The experimental data are collected from multiple studies: (a): QDP-P1 [125]; AMOEBA [159]; SWM6 [159]; TIP4P-QDP [125]; TL6P sk [172]; BK3 [160]; TIP4P-QDP-LJ [126]; TL6P [172]; CC-pol-8s' [158]; uAMOEBA [367]; HBP [190]; TIP4P-QDP [125]; POL4D [159]; iAMOEBA [167]; CC-dpol-8s' [158]; Dang-Chang [152]; TL5P [166]; SWM4-NDP [159]; fm-TIP4P/F-TPSS-D3 [175]; TL4P [166]; TL3P [166]; MFP/TIP3P [149]. (b): MCDHOr [104]; MCDHOff [104]; MCDHOfc [104]; IPOL-0.13-0.1 [118]; APOL-0.13 [118]; COS/D2 [170]; COS/G2 [368]; IPOL-0.16-0.1 [118]; SWM4-NDP [165]; COS/D [128]; IPOL-0.13 [118]; POL3 [118]; COS/B2 [95]; COS/G3 [368]; APOL-0.16 [118]; COS/B1 [95]; IPOL-0.16 [118]; STR/RF [95]; STR/1 [95].…”

An efficient water force field calibrated against intermolecular THz and Raman spectra

“…A multitude of polarizable water force fields have been developed, treating polarizability in many different ways, i.e., Drude oscillator models, [22][23][24][25][26][27] first principle water models, [28][29][30] models including three-body interactions explicitly, 31,32 fluctuating charge models, 33,34 and models with an inducible dipole moment [35][36][37][38][39][40][41][42][43][44] or higher electrostatic moments. 38,45,46 Beyond that-and that is no longer standard for most water models-the electrostatic properties need to be fine-tuned to reproduce accurate transition dipoles as well as transition polarizabilities so that the relative intensities in the THz and Raman spectra agree with experiment. Moreover, the simulation of higher order response functions requires very extensive sampling of phase space, for which simulation times of a few 100 µs are needed; computational efficiency of the model thus is very important.…”