I want to use multiple trajectories in the Simulation Event Analysis script to analyze a Desmond MD simulation. Is there a way I can combine multiple trajectories for use with the script?

Yes, you can use the manipulate_trj.py script that comes with Desmond in Suite 2009 Update 2. This will allow you to merge trajectories. To get a usage statement, type:

$SCHRODINGER/run -FROM desmond manipulate_trj.py -h

The script is documented fully in the Desmond User Manual.

Keywords: Desmond, combining multiple trajectories, MD analysis

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