Effective Time Difference for Biological MD Simulation - Glycine, Alanine, Valine, Leucine and Isoleucine Trimer -

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  • SATO Rei
    Department of Chemistry, Faculty of Science, Josai University
  • TERAMAE Hiroyuki
    Department of Chemistry, Faculty of Science, Josai University
  • ISHIMOTO Takayoshi
    Research Institute for Computational Science, National Institute of Advanced Industrial Science and Technology Core Research for Revolutional Science and Technology, Japan Science and Technology Agency
  • NAGASHIMA Umpei
    Research Institute for Computational Science, National Institute of Advanced Industrial Science and Technology Core Research for Revolutional Science and Technology, Japan Science and Technology Agency

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  • 生体分子の分子動力学シミュレーションにおける効率的な時間刻みの範囲　―　グリシン、アラニン、バリン、ロイシン、イソロイシン３量体　―
  • セイタイ ブンシ ノ ブンシ ドウリキガク シミュレーション ニ オケル コウリツテキナ ジカン キザミ ノ ハンイ グリシン アラニン バリン ロイシン イソロイシン 3リョウタイ

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Abstract

In order to perform an efficient MD simulation for the biosystem, the energy error was investigated changing Δt from 0.02 fs to 3.0 fs for 5 kinds of the amino acid trimers using the Verlet method for integration. Average error is increased proportionally as the square of Δt in this case From 0.5 fs to 1.5 fs, the average error and its standard deviation were almost the same in this case whereas the errors rapidly increased in the range from 0.02 fs to 0.5 fs. No strong difference was observed between 5 amino acid trimers cases, but error accumulated as molecular size increased.

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