• Bulletin of the Korean Chemical Society
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• 제21권4호
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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.

• Bulletin of the Korean Chemical Society
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• 제33권3호
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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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• 제31권12호
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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.

• Bulletin of the Korean Chemical Society
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• 제33권3호
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• pp.893-896
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• 2012

Using molecular dynamics simulation method, we studied the carbon nanotube (CNT) non-covalently interacting with a polymer. As the polymer coiled around the CNT, the diameter of CNT deformed by more than 40% of its original value within 50 ps. By considering three different polymers, we conclude that the interaction between the CNT and polymer is governed by the number of repeating units in the polymer, not by the molecular weight of polymer.

• 한국전산유체공학회:학술대회논문집
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• 한국전산유체공학회 2010년 춘계학술대회논문집
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• pp.581-583
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• 2010

The report summarizes research activities in the Multiscale Energy System Laboratory at Sogang University during September 2009 and February 2010. They are mostly about molecular dynamics simulation of osmotic flows at nanoscale.

• 한국전산유체공학회:학술대회논문집
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• 한국전산유체공학회 2008년도 학술대회
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• pp.204-207
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• 2008

Stochastic molecular dynamics simulation is a variation of standard molecular dynamics simulation that basically omits water molecules. The omission of water molecules, occupying a majority of space, enables flow simulation at microscale. This study reports our stochastic molecular dynamics simulation of particles diffusing in rectangular microchannels. We interestingly found that diffusion patterns in channels with a very small aspect ratio differ by dimensions. We will also discuss the future direction of our research toward a more realistic simulation of micromixing.

• 한국전산유체공학회:학술대회논문집
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• 한국전산유체공학회 2008년 추계학술대회논문집
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• pp.204-207
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• 2008

Stochastic molecular dynamics simulation is a variation of standard molecular dynamics simulation that basically omits water molecules. The omission of water molecules, occupying a majority of space, enables flow simulation at microscale. This study reports our stochastic molecular dynamics simulation of particles diffusing in rectangular microchannels. We interestingly found that diffusion patterns in channels with a very small aspect ratio differ by dimensions. We will also discuss the future direction of our research toward a more realistic simulation of micromixing.

• Bulletin of the Korean Chemical Society
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• 제35권5호
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• pp.1559-1561
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• 2014

• Bulletin of the Korean Chemical Society
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• 제34권3호
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• pp.946-948
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• 2013

• 정보처리학회논문지D
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• 제12D권6호
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• pp.921-930
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• 2005

본 논문에서는 개발된 범용 분자 시뮬레이션 시스템에 대해 기술하고자 한다. 본 연구에서 개발된 분자 시뮬레이션 시스템의 가장 큰 장점은 다른 무엇보다도 Langevin dynamics simulation이나 dissipative particle dynamics simulation 기법을 도입하여 all-atom 모델뿐만 아니라coarse-grain 모델까지도 다룰 수 있도록 설계하였고 따라서 미시영역은 물론 중간영역에서 일어나는 현상까지도 시뮬레이션 할 수 있도록 설계하였다는 점이다. 이를 통해 하나의 통합된 분자 시뮬레이션 시스템으로 생체막 내에서 마취제의 분포, 단백질 접힘 현상, 마이크로 채널 내에서 생체고분자의 구조와 유동 특성 등과 같이 미시영역에서부터 중간영역에 이르는 다양한 현상을 연구할 수 있게 되었다 개발된 시스템을 이용하면 molecular dynamics simulation에 기반한 분자 시뮬레이션 시스템으로는 불가능한 여러 중요한 바이오/나노 시스템을 시뮬레이션 할 수 있을 것으로 기대한다 마지막으로 벤치마크 결과를 통해 개발된 분자 시뮬레이션 시스템의 성능을 측정하였고 성능 최적화를 위한 병목지점을 조사하였다.