(Received: April 26, 2007; Accepted for publication: October 25, 2007; Published on Web: December 3, 2007)
In order to execute molecular dynamics (MD) simulation for the holding process and native structure of proteins efficiently, Hamiltonian algorithm (HA) was equipped to an MD program: PEACH. The difference between the conventional method and HA is evaluated using Leu-Enkephalin and Met-Enkephalin. HA was efficient for sampling a wide area of geometrical space because many low energy conformations were observed along trajectories of HA.
Keywords: Molecular dynamics, Hamiltonian algorithm, Native structure of protein, Holding process of protein, Enkephalin
Text in Japanese