Hi Justin, I am having following doubts regarding umbrella sampling of phosphate ion binding to my protein .
1. As per the tutorial, I need to fix an immobile reference. In my case which region do I have to fix as my protein consists of one single chain. Since I am studying the binding and unbinding of ion, shall I fix the ion fixed. If it's so, then do I have to give a different chain name for it as my complex doesnot chain name for ion/ligand. 2. What should be the size of box and how do I know where to place the protein's COM in box (the precise location). Pls reply so that I can move further with the procedure -- Bharat
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