After I run a Desmond MD simulation, I want to strip water and counter ions from selected frames in the trajectory file and write them out as separate files. How can I do this?

You can use the script trajectory_extract_frame.py, which you can run with this command:

$SCHRODINGER/run -FROM desmond trajectory_extract_frame.py

Use the -h option to display the usage message.

Keywords: Desmond, trajectory, strip waters and ions

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