The Basic Phases of a Trajectory

A given molecular dynamics trajectory can be divided into three sequentially-ordered phases  

Any one of these is optional. The running phase is often thought of as first an equilibration phase and then an averaging phase, although HyperChem does not specifically distinguish these two. 

The heating phase is used to take a molecular system smoothly from lower temperatures, indicative of a static initial (possibly optimized) structure, to the temperature T at which it is desired to perform the molecular dynamics simulation. The run phase then constitutes a simulation at temperature T. If the heating has been done carefully, it may be possible to skip the equilibration phase 

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