[gmx-users] genion deletion edges

[Dallas Warren]

>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?

No, since they are a consequence of the PBC.  If you find a chain that is 
sticking out one side of the box, go to the opposite side and you will see 
a void where it is actually located.

VMD can show adjoining boxes to help with PBC visualisation.

Catch ya,

Dr. Dallas Warren
Research Fellow
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9083
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