Hey :) Just center the bilayer around z=0, solvate and put all molecules in the box with trjconv. Then add 10 to the PBC Z-component (third number from the last line in the .gro file).
Cheers, Tsjerk On Mon, Jun 3, 2013 at 6:55 PM, Gunther Lukat <[email protected]> wrote: > You could try packmol or the MembraneEditor. > > http://www.cellmicrocosmos.org/index_cm2.php > > > Dipl.-Inf. Gunther Lukat > [email protected] > www.aplvoro.org > > > > Am 03.06.2013 um 18:43 schrieb Neha <[email protected]>: > > > Hello everybody, > > > > I am a new user to Gromacs and am working on lipid simulations with the > > Martini forcefield. The Martini website provides a pre-equilibrated DPPC > > bilayer, and I was wondering if there were any told that would allow me > to > > convert this bilayer into a monolayer. For periodic boundary conditions > to > > work, I was thinking of a stack that would go like > > > > Water > > Lipid Heads > > Tails > > Vacuum > > Tails > > Lipid Heads > > Water > > > > Is there any way to split apart the provided bilayer using some > combination > > of Gromacs tools and introduce a space of at least 10 nm which is > apparently > > the distance needed for the tails to not interact with each other? > > > > If there is no way of simply splitting the bilayer, what would you > recommend > > for creating a simulation of lipid monolayers from a single DPPC > molecule? I > > feel like I could use genconf but it might require too much > equilibration. I > > am hopeful that there is some way of simply working with the provided > > bilayer. > > > > Any help would be appreciated! > > > > > > > > -- > > View this message in context: > http://gromacs.5086.x6.nabble.com/Creating-a-monolayer-from-Martini-bilayer-tp5008740.html > > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > > -- > > gmx-users mailing list [email protected] > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [email protected]. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Tsjerk A. Wassenaar, Ph.D. -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
