[gmx-users] Ensuring of periodicity in bilayer simulation

Hideya Nakamura hideyanakamura at gmail.com
Tue Sep 1 19:31:27 CEST 2009

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

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