[gmx-users] About simulating lipid bi-continuous cubic phase

George Khelashvili gek2009 at med.cornell.edu
Wed Nov 3 23:03:54 CET 2010

Dear users,

I am attempting to simulate lipid cubic phase using Coarse grained MD 
from the spontaneous aggregation approach, starting from random mixture 
of lipids in solution, in the spirit of JACS 2009 paper from the Martini 
community. I had several technical issues before setting up the 
simulations and I would appreciate expert opinion on these.

My main concern is about the interplay between the number of lipids in 
the system, initial size of the simulation cell and the pressure 
coupling method to use. What should be the recipe for choosing the 
initial number of lipids? Obviously, I would think that one has to 
choose the number large enough to form at least one unit cell of the 
bi-continuous cubic phase. But what happens if I don't choose exactly 
this "magic" number, but slightly more? Then I would think that after 
running the simulation, the simulation box would contain more than just 
a unit cell of the cubic phase. Can this be a problem?

Also does the initial size of the simulation box matter if one simulates 
spontaneous aggregation process as long as the molecules initially "fit" 
into the box?

And finally, what role should isotropic vs anisotropic pressure coupling 
play in such approach? Which pressure coupling method should be 
preferred in such spontaneous aggregation simulation?

Any advice will be greatly appreciated!

Thank you in advance,


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