Hello GROMACS users, I am trying to compute PMF profile for water by integrating the force profile along a given direction. I take the forces directly from MD. I am using SETTLE for constraining the geometry of water molecules (SPC/E model). My question is that do these forces include the constraint forces or are these simply the forces on individual atoms at a given snapshot. If they do not include the constraint forces, then is there a way to include it because it might affect the dynamics.
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