Thanks for your response,
I'm sorry, but I didn't find any text on the "membrane simulation" page on
the wiki. What I meant by constraining waters in the z-direction is that at
the start of the simulation, I constrained waters in the z-direction so
that they wouldn't fall into the gap between the protein and membrane. In
my case, the gap was large enough that some waters made their way in. I'm
just wondering what I could do to make sure that the lipids aggregate
around the protein properly. Should I manually delete these waters, or will
the waters eventually make their way out during the course of the
simulation.
Many thanks,
Max
On Nov 19 2007, Mark Abraham wrote:
N-J.M. Macaluso wrote:
Hi,
I'm performing a transmembrane protein simulation in an explicit DPPC
bilayer. I manually removed the lipids to accomodate my protein and the
system has undergone 15 ns of equilibration.
In removing the lipids, I a gap betwteen the protein and membrane
resulted. Most of the lipid molecules aggregated around the protein, but
I have found that on one side of the protein, there are some water
molecules that have found their way between the protein and lipid
bilayer. Is there any way of removing these by altering the simulation
parameters, or will I have to remove them manually?
See http://wiki.gromacs.org/index.php/Membrane_Simulations... these
waters may have been present in your initial structure.
I already
constrained the waters in the z-direction at the start of the
simulation, so that didn't work in this case.
I don't understand this.
Mark
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