[gmx-users] Re: periodic_molecule & missing interactions

[Valentina]

Thank you for your reply.

My box is quite small indeed, so my cut-offs are 0.5

If I make a single layer, I would have to run quite a small system in
z-direction. 
My residue box size:    0.62840   0.54421   1.60000   0.00000   0.00000 
-0.31420   0.00000   0.00000   0.00000

My suspect of the problem
In my system I have Al, bonded to 6 OH, and Mg, that is non-bonded, so only
LJ. My nrexcl is set to 2, as I don't have dihedrals. The Al and Mg form a
mesh, that should be infinite in xy-

I am guessing what I have to do is to artificially connect those Mg to OH
with k=0 bonds & angles (?) and then include [ pairs ] of Mg O and Mg H to
be calculated as LJ?

I have a non usual FF, hence cannot figure out how to implement it yet.

Thank you for help, V



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