/ 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?
/>/ I already
/>/ constrained the waters in the z-direction at the start of the
/>/ simulation, so that didn't work in this case.
I am surprised that 15ns is not enough for those waters to leave on their own.
Are you doing anisotropic pressure coupling? If not then this is likely to
fix your problem.
Also, painful as it may be, I suggest starting over from scratch.
It is useful to use make_hole version of gromacs-3.1.2 (search
the list for how to get it and use it) or inflategro.
Finally, ///how many waters are we talking about? I///f you deeply believe that
you have done everything correctly then I suggest at least considering the
possibility that there is something interesting going on.
Chris.
/
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