[gmx-users] Ensuring of periodicity in bilayer simulation

Hideya Nakamura hideyanakamura at gmail.com
Tue Sep 1 21:00:48 CEST 2009

Dear Mark,

> A periodic bilayer system has no "upper" region of water. There's one region
> of water, and one bilayer. If you have too little water, your bilayer
> surfaces will "see" each other.

My system has a region of water, one bilayer and another region of
water along Z-direction.
And periodic boundary condition is applied in xyz-directions.
Is there any problem in my system?

> You'll need to rephrase those questions. I don't understand them.

Sorry for confusing.
As you said, if we have too little water, bilayer surfaces will
interact with each other.
Therefore, I set enough number of waters (43 waters per lipid
molecule) so that the bilayer surfaces were separated adequately.
However, when I set an amphiphilic molecule above the upper surface
(distance between the molecule and the upper surface is closer than
the distance between the molecule and the periodic image of lower
surface across upper Z-boundary) and released it, the molecule
absorbed onto the "lower" surface across upper Z-boundary. I think the
molecule should absorb onto the closer surface, i.e, the upper
I am suspecting this result comes from insufficient separation of
bilayer surfaces across periodic condition.
So, my question is that how many water molecules are used in other
users system and how I can confirm enough separation between surfaces.


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