Dear all, This question is regarding Umbrella sampling. My group 1 is substrate and group 2 protein. Trying to pull the substrate molecule from the active site pocket. In all the cases(for group 2), I used either atom or residue for the center of mass [COM]. Now I want to run a simulation by considering that COM of protein which may be present in the vacuum or in the empty space. In other words, I don't want to fix any atom or residue of the protein but I want to fix an empty space. I was not able to find any solutions regarding this if anyone could help me to figure it, would be great.
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