[gmx-users] Ion flux through membrane protein

[Kutzner, Carsten]

Hi Maximilien,

depending on what exactly the questions are that you like to address, the double-membrane
setup as used in computational electrophysiology setups might be helpful for you.
There is a section in the GROMACS PDF manual about that, and there are these two papers:
http://www.sciencedirect.com/science/article/pii/S0005273616300360
http://www.mpibpc.mpg.de/275657/Kutzner_2011_BPJ_101_809-817.pdf

Best,
 Carsten

> On 26 May 2016, at 10:19, Maximilien LOPES RODRIGUES <maximilien.lopesrodrigues at unamur.be> wrote:
> 
> Dear GROMACS users,
> 
> first of all, thank you for paying attention to my question.
> 
> I have a system containing a membrane protein (porin) that is embedded in a lipid bilayer (XY).
> I would like to investigate the flux of ions (or other solutes like sugar) that can pass through the protein.
> Unfortunately, I don't know the general rules to make a such simulation.
> 
> - Can I just add a higher concentration of ions in one side ? (if yes, should I suppress PBC in Z axis ?)
> - Do I put the counter ions on the same side ?
> - So, do I have to make PBC condition only on XY plan ?
> - Is there an external electrical field to apply ? If yes, how ?
> 
> If you have general tutorial documentation, I would be happy to take a look at it !
> 
> Thank you !
> Kind regards,
> Maximilien Lopes Rodrigues
> 
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