[gmx-users] AFM pulling for PMF calculation

[Nickle Fan]

Dear gmx-users:

I am attempting to calculate the PMF of a small molecule across a membrane.
I am using the AFM method (pulling in the z-direction). I find that during
the simulaiton, the small molecule moves not only in the pulling direction,
but also in the x- and y-direction.

Since Pulling_force = spring_constant * (pos_spring- pos_molecule), one
would need the full position (i.e., not just the z-coordinate) of the small
molecule. However, the pull code output  provides only the z-coordinate of
the molecule. Would this cause a problem, or I am missing something apparent
(e.g., I should really do a 3-D pulling)?

Thanks,

Nick
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