Dear gmx-users: I am performing a PMF calculation using the pull code. I selected one fixed atom as a reference group and constrained another atom with respect to this reference group so that their separation in the x- and z-directions remain constant. After running the simulation, I visualized the trajectory and found that the constrained atom dances around the expected position (it did not drift away though).
Is this expected at all? I had thought that when I constrained the atom with respect to the reference group, its position should remain precisely as defined by the constraints. I am using the NVT ensemble. Cheers, Nick
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