[gmx-users] Setting up a complex membrane simulation
jonas_dehairs at hotmail.com
Fri Nov 2 16:15:29 CET 2012
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.
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