Restart or extend a single stage of a Desmond simulation from Maestro
You can restart or extend a simulation with the same parameters and number of processors using the checkpoint file saved at the end of the simulation. Only a single simulation stage of a Desmond job can be restarted or extended. For example, you might want to restart the production simulation stage if it failed, or extend the simulation time of the production stage.
To restart the simulation from Maestro, follow these steps:
1. Choose Applications → Desmond → Molecular Dynamics
2. Choose Import from file in the Model system section.
3. Click Browse and navigate to the checkpoint file (.cpt) generated by the interrupted simulation. The default name of this file is jobname.cpt.
When the checkpoint file is successfully imported, the Desmond panel enters a read-only state, in which most of the controls are set by the information read and cannot be changed.
4. Increase the total simulation time if necessary (this is the only setting you should adjust).
5. Click the Settings button 
, set the job parameters in the Job Settings dialog box, and click Run to run the job.
To write out the input file and a script for running the job from the command line, click the arrow next to the Settings button and choose Write.
You can also start a new simulation from the output .cms file if you want to change the parameters or the number of CPUs, but this will not strictly continue the previous simulation. This is because the velocity information is saved in the .cpt file but not in the .cms file.