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.
Mark
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