[gmx-users] Simulation problem with extended membrane system!

[chris.neale at utoronto.ca]

It is unclear why your second method works for you. However, given that it does,
just use genbox -cs spc216.gro -cp 183_system_that_worked.gro -box 9.2 9.2 8.3
and then use your own script to remove any spc waters that were put inside the
membrane and modify the nubers in your topology file accordingly.

I imagine that your first attempt didn't work since an entire dppc molecule is
removed upon a single collision and this will lead to "holes" in your membrane
that will quickly fill with water. Of course this should also have happened in
your second attempt... I am not sure what was different there.

You need semiisotropic pressure coupling and you need to stop every once and a
while and remove any water molecules that are inside the membrane. Note that
isotropic Pcoupling in a membrane system (as you have been doing) has the
potential to provide a surface tension (or the opposite) that you have not been
intentionally including and so you can expect your membrane to behave differently.

Chris.