[gmx-users] Ensuring of periodicity in bilayer simulation

Mark Abraham Mark.Abraham at anu.edu.au
Tue Sep 1 19:42:22 CEST 2009

Hideya Nakamura wrote:
> Dear gromacs users,
> I am simulating interaction of lipid bilayer with some large molecules.
> I set molecules above the bilayer (upper leaflet) and then released it
> so that bilayer-molecules interaction was simulated.
> I am now wondering lower leaflet-molecules interaction, i.e,
> interaction across Z-boundary, affects on the upper leaflet-molecules
> interaction causing artificial results.

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 question is how many water molecules are you simulating?
> Now, I am setting 43 waters per lipid molecule, which was determined
> based on literatures.
> Is it enough to ensure of periodicity of Z-direction in bilayer simulation?
> And also, is there any way to determine the enough number of waters?

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


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