[gmx-users] The largest charge group contains [GIANT CRAPTON] of atoms

Alex nedomacho at gmail.com
Thu Apr 2 01:42:23 CEST 2015

I have a custom-FF (OPLSAA based) system with ~8500 atoms, which is a
rectangular graphene sheet with a hole and six pieces of small organics
covalently bound at the hole edge. About 95% of all atoms are electrically
neutral, with the exception of the functional groups mentioned above and a
total of 24 graphene edge carbons (-0.06e), each passivated by a hydrogen
(+0.06e).  All charges have been carefully set (actually, from our own DFT
calculations) to make the system electrically neutral. The charge values
only have two decimals, set in ffnonbonded.

Two issues:

1. x2top yields a total charge of something e-6. I initially ignored it,
but now I think it may be indicative of a actual problem, because:
2. grompp produces a fatal error (see subject) with the number of atoms in
the group ~half the size of the system.

Because I am not using anything out of the box (coordinates, FF), I'm
really perplexed here. I checked the manual, and it makes sense that a
charge group is a way to lump atoms into locally neutral regions. And
that's sort of exactly what I have, at least from the standpoint of
geometry. Definitely not worse than a peptide chain common for GMX.

Any ideas?



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