[gmx-users] flying water on monolayer

Pedro Alexandre Lapido Loureiro paloureiro at biof.ufrj.br
Fri Nov 12 18:10:36 CET 2004

> Hi all (sorry for send it again),
> I'm simulating a monolayer in gromacs 3.2.1. I have a brief question 
> that maybe someone more experimented has just due with. The fact is that 
> everything seems to be all right except that some waters (6 of 20000) 
> fly away from the bottom of the layer of water under the monolayer till 
> reach the the top of the monolayer ( I'm using periodic conditions xyz), 
> some of them remain there some time then they come back to the water 
> layer but in fact there's always an average of water molecules in the 
> top of my monolayer. The  force field that I'm using is GROMACS ( 
> gromos-87 + extended) and the water are SPC. That's normal? there's any 
> way to fix it? There are any  significant change for that I have to take 
> in consideration?
> Thank you, Hector
Hi Hector.

There are two ways to solve this:
1) To impose a potential that keeps the waters in the bulk.
2) To replicate another monolayer in the "top" and to enlarge the Z domension, 
so the lipid tails will only see vacuum:

In this case, even with periodic boundary conditions in Z, tails from the two 
monolayers will not see each other. 



Pedro Alexandre Lapido Loureiro
Laboratório de Física Biológica
Instituto de Biofísica

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