(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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