Journal of Chemical Software
Online ISSN : 1883-8359
Print ISSN : 0918-0761
ISSN-L : 0918-0761
Molecular Dynamics Simulation of Biological Molecules (1) Methods
Yuto KOMEIJIMasami UEBAYASIUmpei NAGASHIMA
Author information
JOURNALS FREE ACCESS

2000 Volume 6 Issue 1 Pages 1-36

Details
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.

Information related to the author
© 2000 by the Chemical Software Society of Japan
Next article
feedback
Top