[gmx-users] genion deletion edges

[dsh2002 at med.cornell.edu]

Hello All,
My system consists of POPC bilayer, solvent water above and below the
membrane and a peptide in the membrane.
I took the POPC patch from a previously equilibrated Larger patch
originally from Tieleman, that has been simulated for some time.  So my
patch does not have very clean edges, meaning some parts of some lipids
protrude out of my boundaries for the box.  Will increasing the box
dimensions so that all of the lipids totally fit in the box mess up the
simulation by decreasing the density of the bilayer?  And does protruding
lipids or atoms mess up the periodic boundary conditions?
I noticed when I used genion to add Cl's to my system, the coordinate file
 seemed to "clean" up the edges of my box by truncating ends of lipids. 
Is this a weird artifact that I have made or is this a general process of
genion?

any insights would be much appreciated.
danny.