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

Rei SATOa, Hiroyuki TERAMAEa*, Takayoshi ISHIMOTOb,c and Umpei NAGASHIMAb,c

aDepartment of Chemistry, Faculty of Science, Josai University
1-1 Keyakidai, Sakado, Saitama 350-0295, Japan
bResearch Institute for Computational Science, National Institute of Advanced Industrial Science and Technology
1-1-1Umezono, Tsukuba, Ibaraki 305-8568, Japan
cCore Research for Revolutional Science and Technology, Japan Science and Technology Agency
4-1-8 Honmchi, Kawaguchi, Saitama 332-0012, Japan

(Received: April 26, 2007; Accepted for publication: June 18, 2007; Published on Web: September 5, 2007)

In order to perform an efficient MD simulation for the biosystem, the energy error was investigated changing Dt 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 Dt 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.

Keywords: Time Difference, Molecular Dynamics, Trimer, Glycine, Alanine, Valine, Leucine, Isoleucine


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