[gmx-users] Creating a monolayer from Martini bilayer

Neha nshafique at wesleyan.edu
Mon Jun 3 18:43:15 CEST 2013

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 

Lipid Heads
Lipid Heads

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

Any help would be appreciated! 

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