[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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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