Transplantation of the PEACH System from UNIX Computer to Windows Computer and Practice in the Simulation of Thermal Denaturation of Proteins

Yoshiro NAKATA*, Toshiharu TAKIZAWA, Minemasa OGINO and Masami UNO

Department of Biophysics, Faculty of Engineering, Gunma University
4-2 Aramaki, Maebashi, 371-8510 JAPAN

(Received: August 4, 2003; Accepted for publication: October 3, 2003; Published on Web: November 27, 2003)

PEACH, a program for molecular dynamics simulation of biochemical molecules, was transplanted from UNIX computer to Windows computer. Visual Fortran was utilized as the compiler. MD simulation of two model proteins, glucagon and prion, was performed at several different temperatures. The structures of 1AG2 and 1GCN were used as initial structures for the simulation. The helix-coil transition was observed in a few nano seconds at 400 K in the case of the glucagon model.

Keywords: Molecular dynamics simulation, PEACH, Parallel computing, Message passing interface (MPICH), Proteins, Thermal denaturation, Glucagon, Prion

Abstract in Japanese

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