[gmx-users] Ion conduction through a protein-membrane system

Peter C. Lai pcl at uab.edu
Tue Oct 2 08:40:36 CEST 2012

On 2012-10-01 11:16:43PM -0700, Shima Arasteh wrote:
>  Dear users,
> I want to study ion conduction through a protein-memrane system. 
> First of all, I tried to simulate a usual protein-membrane system. I'd like to know if it is possible to add asymmetrical number of ions to leaflets of membrane?

Yes. You need to first use trjorder -z to reorder the waters, then you need 
to make 2 index group of consecutive atoms in each layer. Tell genion to only 
pick waters from the separate index groups. It is important that the index
groups representing the water surrounding the "top" and "bottom" leaflet are 
consecutive in atom number or else genion will refuse to run. The easiest way 
to do that is to find Z around the middle of the bilayer where there are 
no waters and separate the top waters from the bottom waters. 

Note that use of pbc=xyz Periodic Boundary Conditions will allow the 
"extracellular" ions to travel into the "intracellular" space as the top ions 
diffuse +Z (and the "intracellular" ions can diffuse -Z into the 
"extracellular" space), so track your ion movements appropriately.

Finally if the total charge of the system isn't balanced, grompp will throw
a notice or a warning. I don't know what the consequences of running a 
simulation of a non-neutral system has on things like energy conservation...

> Secondly, is it possible to  apply an external electrical field to study ion conduction in a system?

The manual appears suggests such a thing might be possible to some extent.
You'll probably want to look for yourself to see if your use-case is supported.

Peter C. Lai			| University of Alabama-Birmingham
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