Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

Density, self-diffusion coefficient, and shear viscosity of pure liquid water are predicted for temperatures between 280 and 373 K by molecular dynamics simulation and the Green–Kubo method. Four different rigid nonpolarizable water models are assessed: SPC, SPC/E, TIP4P, and TIP4P/2005. The pressure dependence of the self-diffusion coefficient and the shear viscosity for pure liquid water is also calculated and the anomalous behavior of these properties is qualitatively well predicted. Furthermore, transport properties as well as excess volume and excess enthalpy of aqueous binary mixtures containing methanol or ethanol, based on the SPC/E and TIP4P/2005 water models, are calculated. Under the tested conditions, the TIP4P/2005 model gives the best quantitative and qualitative agreement with experiments for the regarded transport properties. The deviations from experimental data are of 5% to 15% for pure liquid water and 5% to 20% for the water + alcohol mixtures. Moreover, the center of mass power spectrum of water as well as the investigated mixtures are analyzed and the hydrogen-bonding structure is discussed for different states.

https://thet.uni-paderborn.de/fileadmin/thet/Publikationen/Veroeffentlichungen/Trans_aqueous_alcohol.pdf

Prediction of self-diffusion coefficient and shear viscosity of water and its binary mixtures with methanol and ethanol by molecular simulation.

Terahertz (THz) radiation interacts strongly with the intermolecular hydrogen-bond network in aqueous liquids. The dielectric properties of liquid water and aqueous solutions in the THz spectral region are closely linked to the microscopic dynamics of the liquid solution, and hence THz spectroscopy offers an important insight into fundamental intermolecular interactions in polar liquids. At the same time, the strong and characteristic interaction between THz radiation and liquids offers a methodology for the classification of liquids inside containers, and hence the THz region is suitable for remote detection of some of the properties of bottled liquids. Here we present a review of THz spectroscopy and modeling of water-ethanol mixtures, and establish a link between the dielectric function of water-ethanol mixtures and some of their thermodynamic properties. We then review how the knowledge of the dielectric function of aqueous mixtures can be used for inspection of liquids inside bottles. Finally we draw up some of the limits to the applicability of THz reflection spectroscopy in the identification of dangerous liquids.

Terahertz reflection spectroscopy of Debye relaxation in polar liquids [Invited]

Recently we have investigated the storage and adsorption selectivity of CO2 and CH4 in three different classes of nanoporous materials—silicalite, IRMOF-1, and C168 schwarzite through Monte Carlo simulation (Babarao, R.; Hu, Z.; Jiang, J. Langmuir, 2007, 23, 659). In this work, the self-, corrected, and transport diffusivities of CO2 and CH4 in these materials are examined using molecular dynamics simulation. The activation energies at infinite dilution are evaluated from the Arrhenius fits to the diffusivities at various temperatures. As loading increases, the self-diffusivities in the three frameworks decrease as a result of the steric hindrance; the corrected diffusivities remain nearly constant or decrease approximately linearly depending on the adsorbate and framework; and the transport diffusivities generally increase except for CO2 in IRMOF-1. The correlation effects are identified to reduce from MFI, C168 to IRMOF-1, in accordance with the porosity increasing in the three frameworks. Predictions o...

Diffusion and Separation of CO2 and CH4 in Silicalite, C168 Schwarzite, and IRMOF-1: A Comparative Study from Molecular Dynamics Simulation

This work highlights a variety of peculiar characteristics of adsorption and diffusion of polar molecules such as water, methanol and ethanol in zeolites. These peculiarities are investigated with the aid of configurational-bias Monte Carlo (CBMC) simulations of adsorption isotherms, and molecular dynamics (MD) simulations of diffusivities in FAU, MFI, DDR, and LTA zeolites.Because of strong hydrogen bonding, significant clustering of the guest molecules occurs in all investigated structures. Because of molecular clustering, the inverse thermodynamic factor 1/Γi ≡ (d[ln ci])/(d[ln fi]) exceeds unity for a range molar concentrations ci within the micropores. The degree of clustering is lowered as the temperature is increased. For the concentration ranges for which 1/Γi > 1, the Fick diffusivity, Di, for unary diffusion is often lower than both the Maxwell−Stefan, Đi, and the self-diffusivity, Di,self. For water−alcohol mixtures, the hydrogen bonding between water and alcohol molecules is much more predomin...

Hydrogen bonding effects in adsorption of water-alcohol mixtures in zeolites and the consequences for the characteristics of the Maxwell-Stefan diffusivities

Molecular dynamics simulation of ethanol/water mixtures for structure and diffusion properties

Ion-pairing and aggregation of ionic liquid-neutralized polyoxometalate salts in aqueous solutions

Morphology and structure transition of surfactant/scCO2 system: A dissipative particle dynamics simulation

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Papers

Molecular dynamics simulation of ethanol/water mixtures for structure and diffusion properties

Ion-pairing and aggregation of ionic liquid-neutralized polyoxometalate salts in aqueous solutions

Morphology and structure transition of surfactant/scCO2 system: A dissipative particle dynamics simulation