• 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.

• 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.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.

• Bulletin of the Korean Chemical Society
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• v.33 no.3
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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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• 2010.05a
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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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• 2008.03a
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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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• 2008.10a
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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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• v.35 no.5
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• pp.1559-1561
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• 2014

• Bulletin of the Korean Chemical Society
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• v.34 no.3
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• pp.946-948
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• 2013

• The KIPS Transactions:PartD
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• v.12D no.6 s.102
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• pp.921-930
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• 2005

In this paper, a general purpose molecular simulation system which has been developed by the author, are described. One of the most advantageous features is that the molecular simulation system can handle a coarse-grained model as well as an all-atom mode. Therefore, we can simulate mesoscopic phenomena as well as microscopic phenomena with the help of Langevin dynamics simulation and dissipative particle dynamics simulation techniques. Thus we could study anesthesia, protein folding, biopolymer flow in microchannel with single framework, which spans from microscopic to mesoscopic scales. We expect that we can also simulate many other bio/nano systems of technological importance which are not feasible by means of molecular dynamics simulation technique. Finally, performance data are shown and a bottleneck is identified for future optimization.