If I restart a Desmond job from a checkpoint file (.cpt) from the same directory, will it overwrite the current trajectory?

Desmond will not overwrite the trajectory, and will in fact refuse to launch, issuing a response like:

testl_trj exists on submit node.
please run the job from another directory.

To safely restart your job, move the .cfg and .cpt file to a different directory and launch from that directory, or rename the .cfg and .cpt files. This will avoid a naming collision with the original trajectory.

Keywords: restart trajectory checkpoint .cpt overwrite Desmond

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