Hi, Dunno, never tried the walls code.
Mark On Thu, Jul 2, 2015 at 11:37 PM João Martins <joaomartins...@gmail.com> wrote: > As a completely pointless point since Mark just explained why it doesn't > make much sense to do it, you can achieve the same by separating your > waters in the [ molecules ] directive, calling each whatever group name you > define on your index file. Then you can use genion for each subset of > waters, which will only replace waters within each of the molecule subsets > you defined. > > @Mark > > Would this be possible with pbc = xy and nwall = 2? I'm quite sure > energetically it wouldn't make much sense, but I think it would indeed > succeed on keeping the ions in the correct membrane side. > > Best regards, > João Martins > > > > *Joao Martins* > > joaomartins...@gmail.com > > On Thu, Jul 2, 2015 at 11:01 PM, Mark Abraham <mark.j.abra...@gmail.com> > wrote: > > > Hi, > > > > Your membrane is probably in the x-y plane, so you just insert ions > > everywhere and delete from the .gro file all that have a z coordinate > > bigger than whatever value aligns with the bottom of your membrane, and > > correct the number of atoms in the .gro and .top file accordingly. > > > > This won't help you because you only have a single chunk of water, so > your > > concentration differential will just diffuse away. You could use > > flat-bottomed position restraints in GROMACS 5 to help with that, > perhaps. > > Or the Computational Electrophysiology feature. > > > > Mark > > > > On Thu, Jul 2, 2015 at 7:37 PM anu chandra <anu80...@gmail.com> wrote: > > > > > Dear Gromacs users, > > > > > > I am working with membrane proteins. I have build my membrane-protein > > > systems with a layer of water bed on top and bottom of the membrane. > > Now, > > > I would like to add a specific concentration of KCl to bottom layer of > > the > > > water bed. Can anybody suggest me a way to add ions to a specific water > > > layer of the membrane-protein system? > > > > > > Thanks in advance > > > > > > Anu > > > -- > > > 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. > > > > > -- > > 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. > > > -- > 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. -- 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.