[gmx-users] Umbrella sampling and PMF calculations

[Alex]

>>
>
> 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