In this study we have investigated the determination of proper time step in
molecular dynamics simulation. Since the molecular dynamics is mathematica
lly related to nonlinear dynamics, the analysis of eigenvalues is used to e
xplain the relationship between the time step and dynamics. The tracings of
H-2 and CO2 molecular dynamics simulation agrees very well with the analyt
ical solutions. For H-2, the time step less than 1.823 fs provides stable d
ynamics. For CO2, 3.808 fs might be the maximum time step for proper molecu
lar dynamics. Although this results were derived for most simple cases of h
ydrogen and carbon dioxide, we could quantitatively explain why improperly
large time step destroyed the molecular dynamics. From this study we could
set the guide line of the proper time step for stable dynamics simulation i
n molecular modeling software.