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? Thanks, Alex -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
