[gmx-users] Setting up a complex membrane simulation

Justin Lemkul jalemkul at vt.edu
Fri Nov 2 16:21:54 CET 2012

On 11/2/12 11:15 AM, jonas87 wrote:
> Dear all,
> I wish to run a simulation of a membrane consisting of about 10 different
> lipids.
> Through the automated topology builder ( example
> <http://compbio.biosci.uq.edu.au/atb/download.py?molid=1556>  ) I can obtain
> of each lipid a structure file in pdb format (it has one single molecule)
> and an .itp topology file.
> I want to make a random mix of these lipids with water and let it
> equilibrate over 300 us or so to let it assemble into a bilayer.
> My question is, how can I combine all these structures and topologies into
> one system that has X molecules of lipid A, Y molecules of lipid B, etc. I
> think genbox might have the answer for combining the sructures, but how?

Building lipid membranes is complicated.  In theory, you could position 
individual molecules in specific orientations within a given box with editconf 
to form patches that can then be translated and rotated in any way you desire, 
or replicated with genconf -nbox.  I have only ever done this for a 
single-component lipid membranes.

The topology is actually easier.  After #including the parent force field, you 
simply #include each lipid topology individually.  The [molecules] section then 
must reflect the contents of the coordinate file with respect to the number of 
molecules and the order they appear.

> Also, if someone could point me towards a tutorial were they let a membrane
> form from a random distribution of a lipid with water that would be useful.
> The only GROMACS membrane tutorials that I can find always start with
> pre-equilibrated membranes of 128 DOPC molecules.

To my knowledge, there is no such tutorial (if it's not on the Tutorials page or 
found via Google, it doesn't exist).  You can randomly insert molecules into a 
box with genbox -ci -nmol and then fill with solvent later.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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