[gmx-users] Ensuring of periodicity in bilayer simulation

Justin A. Lemkul jalemkul at vt.edu
Tue Sep 1 21:22:33 CEST 2009

Hideya Nakamura wrote:
> 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
> surface.

If the bilayer is homogeneous, then this shouldn't be a problem.  The molecule 
you're using is seeing lipid either way.

> 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.

The size of a system will depend upon the size and orientation of the molecule 
in solution, as well as your cutoff parameters (to satisfy the minimum image 
convention), and how far apart the initial placement is.  So there really isn't 
a single answer that might easily be applied to your system.


> Hideya
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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