[gmx-users] Ion flux through membrane protein

Maximilien LOPES RODRIGUES maximilien.lopesrodrigues at unamur.be
Thu May 26 10:19:56 CEST 2016

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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