[gmx-users] PBC in a closed box.

[Rodney Versace Babilonia]

Hi all,

I am trying to simulate the effusion process of water through hole in a very thin film. The film is partitioning the water box, I wish to count the numbers of waters before and after the simulation in each compartment, but I am afraid that the use of periodic boundary conditions will make waters from one side going to the other side through the boundaries and that affect my counting, in case I turn off the PBC, what kind of electrostatic treatment should I use?

Thanks

-Rod