[gmx-users] COMPEL question: Channel filter outside membrane, how to orient compartment boundaries

[Erik Henze]

Hi,
I am attempting to study permeation events in an ion channel where the
filter is located in the extracellular region, far away from the middle of
the transmembrane regions. My question is two-fold:

1) Where is the optimal place to set up the compartment boundaries?

If I place the compartment boundaries in the middle of the membrane (as
where most channel filters would approximately be) then, given that the
pore of the channel is very large in this region, I will be swapping lots
of ions which aren't actually permeating the channel. This doesn't
necessarily seem like a problem, given that COMPEL can record the
permeation events separately with the cylinder you define. I was concerned,
however, that this constant swapping that COMPEL has to do will make the
simulation very computationally costly/inefficient in some way. This brings
me to my next question:

2) Can you define the cylinder in a way that is independent of the center
of the channel, so that I can place the cylinder in a region centered near
the extracellular region?

Any thoughts/advice on this would be greatly appreciated, thanks!
-Erik H