I have two trajectories that I want to merge and view in Maestro. Is there a way to do that?

Yes. Use the manipulate_trj.py script to merge the trajectories:

$SCHRODINGER/run -FROM desmond manipulate_trj.py [--icms cms-file] [--mode merge|concat] output_trj input-trj1 [input-trj2]

Make sure to specify a .cms file using the --icms option. Otherwise, you will not be able to view the resulting trajectory in Maestro, or run a simulation event analysis. You may use a cms file from either simulation. manipulate_trj.py will not overwrite your original .cms file. See section 9.2 of the Desmond User Manual for details.

Keywords: Desmond

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