Yes, because if your ion diffuses laterally (or whatever constitutes
your "hole"), then you're not sampling what you think you're
sampling. That's what the cylinder geometry is for. You have a
system capable of significant lateral movement, so if you fail to
apply a bias that acts in the x-y plane, your results are very quickly
going to become garbage.
-Justin
Of course. I actually realized that you used COM distance and not e.g.
direction-periodic (which won't accept zero pulling rates anyway) only
after I asked.
Specifying somewhat awkward structures like disks as references could be
avoided by simply allowing a component of the COM distance vector and
not the entire vector) to be used. Anyway, doesn't really matter.
Thanks,
Alex
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