[gmx-users] Re: periodic_molecule & missing interactions

Valentina 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

View this message in context: http://gromacs.5086.x6.nabble.com/periodic-molecule-missing-interactions-tp5010815p5010851.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.

More information about the gromacs.org_gmx-users mailing list