[gmx-users] Ensuring of periodicity in bilayer simulation

[Hideya Nakamura]

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.

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?

Thank you in advance for you help.

Hideya



___________________________________________________________________
Hideya Nakamura, Ph.D.
Post Doctoral Associate
University of Florida, Particle Engineering Research Center (PERC)