Q:

I have a 150 ps Dynamics (Production) simulation run, and then continued with another 50 ps production run. Is there any way I can combine the two runs and view the Potential Energy vs. Time chart for the total of 200 ps?

A:

Yes you should be able to combine the trajectory conformations from the two runs together in the following way:

Open the 150 ps run output .dsv file in the Molecule window first, note that the number of rows in the Conformation tab of the Data table corresponds to the number of conformations in the trajectory.

Use the Structure > Animation > Load command, navigate to the directory of the 50 ps run Output folder and open the .dcd file (or .dsv, either will work). This will load the conformations from the 50 ps run appending them to the existing conformations in the same window. You will now have all the conformations and can use the Chart Plot command for the combined trajectory.