If you run a molecular dynamics simulation with the Standard Dynamics Cascade protocol you may want to check the Equilibration phase to see that the energies have stabilized. When the protocol is run with the option to Save the Intermediate Directory turned on (under the Options button or as a general setting under Edit>Preferences>Protocols) the Intermediate folder containing the details of the different steps of the simulation is available from the client. To plot the energies for the equilibration follow these steps:
1. Open the input dsv file for the Standard Dynamics Cascade job in the Discovery Studio client.
2. Go to the Structure>Animation>Load menu.
3. In the Choose an Animation File panel that appears browse to the *_eq.dcd file in the Intermediate\\4_Equilibration folder for the run and click Open. This adds the equilibration trajectory frames to the Conformations tab of the data table. You can now plot the energies against time or step number using the Chart menu options.