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Article ID: 1007 - Last Modified:

Can I view a Desmond trajectory while a simulation is still running?

Yes. To do this, you will first need to locate the necessary files in the scratch directory where the master job is running. To locate that directory, open the Monitor panel in Maestro, and select the master job. The Host column in the list of jobs tells you the host on which the job is running. The Job Directory field in the Job summary window shows you the scratch directory where the temporary files are located.

You will need the following files and directory from the scratch directory where the master job is running:

  • jobname-out.cms
  • jobname-out.idx
  • jobname_trj/

You may want to copy these back to your workstation, so that you can view the trajectory there (these files will eventually be transferred back, but only at the end of the job). The last item in the list above is actually a directory, and before copying it, we recommend zipping it into an archive:

zip -r jobname_trj

This command creates a .zip file, which is easier to copy. To unzip the file once it has been copied to the workstation:


Once all three files are present in the same directory on the workstation, you can start Maestro, import the jobname-out.cms file, and then click the T button in the Title column of the Project Table to open the trajectory viewer.

Keywords: Desmond, trajectory

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