[gmx-users] Ion flux through membrane protein

Kutzner, Carsten ckutzne at gwdg.de
Thu May 26 10:33:32 CEST 2016

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:


> 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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