Molecular Dynamics Simulation of Biological Molecules (1) Methods

Yuto KOMEIJIa,c*, Masami UEBAYASIb and Umpei NAGASHIMAa

aNational Institute for Advanced Interdisciplinary Research,
1-1-4 Higashi, Tsukuba, 305-8562 Japan
bNational Institute of Bioscience and Human-Technology,
1-1-3 Higashi, Tsukuba, 305-8566 Japan
cElectrotechnical Laboratory
1-1-4 Umezono, Tsukuba, 305-8568 Japan

(Received: June 10, 1999 ; Accepted for publication: June 30, 1999 ; Published on Web: September 20, 1999)

Molecular dynamics simulation has been extensively applied to analyses of structure, dynamics, and function of biological molecules. Various methods implemented in a newly developed software, PEACH (Program for Energetic Analysis of bioCHemical molecules), are described. This review covers: (1) an outline of classical molecular dynamics, (2) generation of the initial structure and temperature, (3) computation of force and potential, (4) time integration, (5) ensemble, and (6) analyses of the generated trajectories.

Keywords: Program for Energetic Analysis of bioCHemical molecules (PEACH), GRAvity piPE (GRAPE), Molecular dynamics, Proteins, DNA, RNA

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