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Hi,
I am done running the md simulation until the end of production md following this tutorial : Protein-Ligand Complex by Justin Lemkul. But, do I need to follow the analysis part in that tutorial? and if I want to analyze in Desmond by SID like this tutorial (3. Molecular Dynamic Simulation Result Analysis on Desmond by Simulation Interaction Diagram (SID) - YouTube), what files do I need to save as output?
Really appreciate any help, thank you.