• Title/Summary/Keyword: Molecular dynamics

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Determination of Proper Time Step for Molecular Dynamics Simulation

  • Jo, Jong Cheol;Kim, Byeong Cheol
    • 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.

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Phase Transition of Confined Gold Nanoparticles: Replica Exchange Molecular Dynamics Study

  • Kim, Hyun-Sik;Li, Feng-Yin;Jang, Soon-Min
    • 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.

Accelerating Molecular Dynamics Simulation Using Graphics Processing Unit

  • Myung, Hun-Joo;Sakamaki, Ryuji;Oh, Kwang-Jin;Narumi, Tetsu;Yasuoka, Kenji;Lee, Sik
    • 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.

Hydrogen Bonds in GlcNAc( β1,3)Gal( β)OMe in DMSO Studied by NMR Spectroscopy and Molecular Dynamics Simulations

  • Shim, Gyu-Chang;Shin, Jae-Min;Kim, Yang-Mee
    • Bulletin of the Korean Chemical Society
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    • v.25 no.2
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    • pp.198-202
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    • 2004
  • Hydrogen bond is an important factor in the structures of carbohydrates. Because of great strength, short range, and strong angular dependence, hydrogen bonding is an important factor stabilizing the structure of carbohydrate. In this study, conformational properties and the hydrogen bonds in GlcNAc( ${\beta}$1,3)Gal(${\beta}$)OMe in DMSO are investigated through NMR spectroscopy and molecular dynamics simulation. Lowest energy structure in the adiabatic energy map was utilized as an initial structure for the molecular dynamics simulations in DMSO. NOEs, temperature coefficients, SIMPLE NMR data, and molecular dynamics simulations proved that there is a strong intramolecular hydrogen bond between O7' and HO3' in GlcNAc( ${\beta}$1,3)Gal(${\beta}$)OMe in DMSO. In aqueous solution, water molecule makes intermolecular hydrogen bonds with the disaccharides and there was no intramolecular hydrogen bonds in water. Since DMSO molecule is too big to be inserted deep into GlcNAc(${\beta}$1,3)Gal(${\beta}$)OMe, DMSO can not make strong intermolecular hydrogen bonding with carbohydrate and increases the ability of O7' in GlcNAc(${\beta}$1,3)Gal(${\beta}$)OMe to participate in intramolecular hydrogen bonding. Molecular dynamics simulation in conjunction with NMR experiments proves to be efficient way to investigate the intramolecular hydrogen bonding existed in carbohydrate.

Molecular Dynamics and Quantum Chemical Molecular Dynamics Simulations for the Design of MgO Protecting Layer in Plasma Display Panel

  • Kubo, Momoji;Serizawa, Kazumi;Kikuchi, Hiromi;Suzuki, Ai;Koyama, Michihisa;Tsuboi, Hideyuki;Hatakeyama, Nozomu;Endou, Akira;Takaba, Hiromitsu;Kajiyama, Hiroshi;Shinoda, Tsutae;Miyamoto, Akira
    • 한국정보디스플레이학회:학술대회논문집
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    • pp.1049-1052
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    • 2008
  • We developed novel molecular dynamics and quantum chemical molecular dynamics simulators for the design of MgO protecting layer in plasma display panel. These simulators were applied to the investigations on the destruction processes of the MgO protecting layer as well as the evaluation of its second electron emission ability. From the simulation results, we successfully proposed new guidelines for MgO protecting layer with high durability and high second electron emission ability.

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