[gmx-users] Creating a monolayer from Martini bilayer

[Gunther Lukat]

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! 
> 
> 
> 
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