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