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

[Kutzner, Carsten]

Hi Erik,

I am not sure that the CompEl code as it is can deal with the setup
you are describing (but I may be wrong).

Below are a few thoughts and things you might want to try.

> Am 24.04.2020 um 00:05 schrieb Erik Henze <ekh58 at cornell.edu>:
> 
> 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?
The compartment boundaries should always be within the membranes,
otherwise the exchanges of waters with ions won't make any sense
as the system is effectively short-circuited.

> 
> 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.
No, probably not, because typically you check for that every 100+ steps,
so it will only be a small performance penalty.

> 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?
You can try with the cyl-up and cyl-down settings and adjust the bulk-offset
parameter accordingly (look at Fig. 3 in 
https://pure.mpg.de/rest/items/item_2249662_6/component/file_2399280/content
for the meaning of these parameters).

Best,
  Carsten

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