[gmx-users] About simulating lipid bi-continuous cubic phase
gek2009 at med.cornell.edu
Wed Nov 3 23:03:54 CET 2010
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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