I would like to view an MD trajectory generated by Desmond while the simulation is still in progress. I loaded the jobname-out.cms file into the Maestro Project Table. When I clicked the "T" button, a message regarding a missing trajectory file jobname_trj.idx appeared. When I tried to import the file with the "Import File" button, Maestro crashed. What is the problem?

First, verify that you are loading your "partial trajectory" jobname-out.cms file via Project → Import Structures, and not via Desmond → Molecular Dynamics → Import from File (which would be incorrect), and that it shows up in the Project Table as a single entry "full system" and not as a group of entries under "_desmond_scratch_donotchange".

If you have loaded the .cms file correctly, the problem could be due to lack of access to *.trj files that are generated in the local scratch space of the node that is physically running the job.

Make a copy of the *_trj directory for the partially-complete trajectory, and place this copy in the Maestro working directory that also contains a copy of *.cms and *.idx. That way, the path specified in .idx matches the location of the *_trj directory. After taking these steps, you should be able to view the partial trajectory.

Keywords: partial trajectory, memory access error, *.trj, Maestro, Desmond

Back to Search Results