Hello I'm currently running a SMD, and according to the standard strategy by Grubmuller H, I should restrain/contrain the center of mass of the protein A while I pull away the ligand or another protein B binding to it, so that the average position of A is kept in place in the process, while rotation and internal movement of A is still allowed. I wonder if it's possible to do this in gromacs. Anyway, the pricinple and algorithm is extremely simple, but I just can't find a detailed description of implementing it in gromacs. Thanks in advance.
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