The molecular dynamics simulation method has been used quite successfully for the study of various kinetic and thermodynamic properties of proteins. However, it can only be applied to simulating motions of small time scales if the simulation is conducted at an atomic level because the time scale for atomic vibration is too small (in order of 1e-15sec). However, proteins do have quite separated length scales ranging from atoms to residuals and from secondary structures to protein domains. At each of these length scales, the corresponding time scales are different. Larger time steps can certainly be taken in simulation at higher level length scales, but the physics at levels beyond atoms is not as clear.
