[gmx-users] Re: periodic_molecule & missing interactions
valentina.erastova at durham.ac.uk
Fri Aug 30 11:32:27 CEST 2013
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
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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