Hello, This is the second time I am sending this message. I have a protein which has a few Thr residues on one side of itself. I would like to know how should I setup mt index file and use which GROMACS tools to calculate potential energy and Sg of water molecules that only face these residues as a function of space coordinate such as z (not radial coordinate r), assuming I want my Thr residues be at the z=0 of the profile of Sg vs. z or PE vs z. Thanks for your helps.
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