[gmx-users] Hydrogens moving inside ring?

[Joanna Bailey]

I am running a molecule which includes a triazine ring, where two of the 
nitrogens have hydrogens and two of the carbons are part of carbonyl 
groups.  When I run the energy minimisation, which converges, the hydrogens 
end up inside the ring with the ring remaining flat. Obviously there is 
something very wrong, I have checked the dihedrals both improper and proper 
and the bond angles, all seems fine. Is there anything else anyone could 
suggest could be the problem? Thank you.

Jo