生体分子の分子動力学シミュレーション(1)方法

古明地 勇人; 上林 正巳; 長嶋 雲兵

doi:10.2477/jchemsoft.6.1

Molecular Dynamics Simulation of Biological Molecules (1) Methods

Yuto KOMEIJI, Masami UEBAYASI, Umpei NAGASHIMA

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

JOURNAL FREE ACCESS

2000 Volume 6 Issue 1 Pages 1-36

DOI https://doi.org/10.2477/jchemsoft.6.1

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Abstract

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.

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