• Bulletin of the Korean Chemical Society
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• v.21 no.4
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• pp.419-424
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• 2000

In this study we have investigated the determination of proper time step in molecular dynamics simulation.Since the molecular dynamics is mathematically related to nonlinear dynamics, the analysis of eigenvalues isused to explain the relationship between the time step and dynamics. The tracings of H2 and CO2 molecular dynamics simulation agrees very well with the analytical solutions. For H2, the time step less than 1.823 fs pro-vides stable dynamics. ForCO2, 3.808 fs might be the maximum time step for proper molecular dynamics. Al-though this results were derived for most simple cases of hydrogen and carbon dioxide, we could quantitatively explain why improperly large time step destroyed the molecular dynamics. From this study we could set the guide line of the proper time step for stable dynamics simulation in molecular modeling software.

• Proceedings of the Korean Society of Potoscience Conference
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• 2005.06a
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• pp.42-42
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• 2005

• Bulletin of the Korean Chemical Society
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• v.33 no.3
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• pp.929-932
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• 2012

The classical molecular dynamics simulation was used to study the phase transition of gold nanoparticles under confinement using Sutton-Chen (SC) potential. Metal gold nanoparticles with different number of atoms are subject to replica exchange molecular dynamics simulation for this purpose. The simulation showing the solidto-liquid melting temperature largely remains unaffected by confinement, while the confinement induces characteristic pre-melting at very low temperature depending on atom number in nanoparticles.

• Bulletin of the Korean Chemical Society
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• v.28 no.10
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• pp.1697-1704
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• 2007

We present results for transport properties of diatomic fluids by isothermal-isobaric (NpT) equilibrium molecular dynamics (EMD) simulations using Green-Kubo and Einstein formulas. As the molecular elongation of diatomic molecules increases from the spherical monatomic molecule, the diffusion coefficient increases, indicating that longish shape molecules diffuse more than spherical molecules, and the rotational diffusion coefficients are almost the same in the statistical error since random rotation decreases. The calculated translational viscosity decreases with the molecular elongation of diatomic molecule within statistical error bar, while the rotational viscosity increases. The total thermal conductivity decreases as the molecular elongation increases. This result of thermal conductivity for diatomic molecules by EMD simulations is again inconsistent with the earlier results of those by non-equilibrium molecular dynamics (NEMD) simulations even though the missing terms related to rotational degree of freedom into the Green-Kubo and Einstein formulas with regard to the calculation of thermal conductivity for molecular fluids are included.

• Bulletin of the Korean Chemical Society
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• v.24 no.6
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• pp.837-842
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• 2003

In ab initio molecular dynamics, whenever information about the potential energy surface is needed for integrating the equations of motion, it is computed “on the fly” using electronic structure calculations. For Born-Oppenheimer methods, the electronic structure calculations are converged, whereas in the extended Lagrangian approach the electronic structure is propagated along with the nuclei. Some recent advances for both approaches are discussed.

• Bulletin of the Korean Chemical Society
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• v.25 no.5
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• pp.737-741
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• 2004

We presents new results for transport properties of dumbbell fluids by equilibrium molecular dynamics (EMD) simulations using Green-Kubo and Einstein formulas. It is evident that the interaction between dumbbell molecules is less attractive than that between spherical molecules which leads to higher diffusion and to lower friction. The calculated viscosity, however, is almost independent on the molecular elongation within statistical error bar, which is contradicted to the Stokes' law. The calculated thermal conductivity increases and then decreases as molecular elongation increases. These results of viscosity and thermal conductivity for dumbbell molecules by EMD simulations are inconsistent with the earlier results of those by non-equilibrium molecular dynamics (NEMD) simulations. The possible limitation of the Green-Kubo and Einstein formulas with regard to the calculations of viscosity and thermal conductivity for molecular fluids such as the missing rotational degree of freedom is pointed out.

• Journal of Advanced Marine Engineering and Technology
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• v.31 no.8
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• pp.932-938
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• 2007

The interaction between adherent molecules and gas molecules was modeled in molecular scale and simulated by the molecular dynamics method in order to understand the evaporation and removal processes of adherent molecules on metallic surface using high temperature gas flow. Methanol molecules were chosen as adherent molecules to investigate effects of adhesion quantify and gas molecular collisions because the industrial oil has too complex structures of fatty acid. The effects of adherent quantify, gas temperature and surface temperature for the evaporation rate of adherent molecules and the molecular removal mechanism were investigated and discussed in the present study. Evaporation and removal rates of adherent molecules from metallic surface calculated by the molecular dynamics method showed the similar dependence on surface temperature shown in the experimental results.

• Bulletin of the Korean Chemical Society
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• v.31 no.12
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• pp.3639-3643
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• 2010

We have developed CUDA-enabled version of a general purpose molecular dynamics simulation code for GPU. Implementation details including parallelization scheme and performance optimization are described. Here we have focused on the non-bonded force calculation because it is most time consuming part in molecular dynamics simulation. Timing results using CUDA-enabled and CPU versions were obtained and compared for a biomolecular system containing 23558 atoms. CUDA-enabled versions were found to be faster than CPU version. This suggests that GPU could be a useful hardware for molecular dynamics simulation.

• Journal of the Semiconductor & Display Technology
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• v.12 no.1
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• pp.61-65
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• 2013

We investigated the wearable dynamics of diamond spherical abrasive during the substrate surface polishing under the pad compression via classical molecular dynamics modeling. We performed three-dimensional molecular dynamics simulations using the Morse potential functions for the copper substrate and the Tersoff potential function for the diamond abrasive. The pad hardness had a big impact on the wearable dynamics of the abrasive. The moving speed of the abrasive decreased with increasing hardness of the pad. As the hardness decreased, the abrasive was indented into the pad and then the sliding motion of the abrasive was increased. So the pad hardness was greatly influenced on the slide-to-roll ratio as well as the wearable rate.

• Journal of the Semiconductor & Display Technology
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• v.10 no.3
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• pp.49-52
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• 2011

This paper shows the results of classical molecular dynamics modeling for the interaction between spherical nano abrasive and substrate in chemical mechanical polishing processes. Atomistic modeling was achieved from 3-dimensional molecular dynamics simulations using the Morse potential functions for chemical mechanical polishing. The abrasive dynamics was modeled by three cases, such as slipping, rolling, and rotating. Simulation results showed that the different dynamics of the abrasive results the different features of surfaces. The simulation concerning polishing pad, abrasive particles and the substrate has same results.