On Thu, Oct 13, 2022, Fanyu Zhao via AMBER wrote:
>
>I encountered a separation of protein and ligand during TI simulation.
I don't think we have enough information to be of any help remotely. You
should re-run the lamba window that saw the separation, save trajctory
snapshots relatively often, and visualize what is going on. Do the same
thing for a lambda value where the ligand did what you expected/wanted it to
do. See if you can figure out what is going on.
....good luck....dac
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Received on Fri Oct 14 2022 - 09:30:03 PDT
