[gmx-users] Setting up a complex membrane simulation

Christopher Neale chris.neale at mail.utoronto.ca
Fri Nov 2 18:20:41 CET 2012

Whatever method you use to set up your system, and be it atomistic or coarse-grained, I suggest that you
build at least 2 such systems independently and run them all for the same amount of time. Looking at convergence 
from the same starting structure with different initial velocities is not nearly as useful as looking at convergence 
from two independent starting conformations.


-- original message --

I wish to run a simulation of a membrane consisting of about 10 different
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?
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.

Best regards,

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