[gmx-users] Creating a monolayer from Martini bilayer

[Tsjerk Wassenaar]

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 <g.lukat at gmx.net> wrote:

> You could try packmol or the MembraneEditor.
>
> http://www.cellmicrocosmos.org/index_cm2.php
>
>
> Dipl.-Inf. Gunther Lukat
> g.lukat at gmx.net
> www.aplvoro.org
>
>
>
> Am 03.06.2013 um 18:43 schrieb Neha <nshafique at wesleyan.edu>:
>
> > 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.
> > --
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-- 
Tsjerk A. Wassenaar, Ph.D.