[gmx-users] Umbrella sampling of phosphate ion binding

[bharat gupta]

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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