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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.