How to run two stages(equilibration+data collection) MD simulation

Hi all

I want to run a MD simulation which consists of  two stages: equilibration and data collection(equilibrium dynamic trajectory data record), is there any body know how to do that? Should I copy the .xsd or .xtd file got from the equilibration run to a new 3D atomistic document. xsd then perform another MD run? Is there any other detail I have to pay attention to?

Thank you.

Jing