Verlet option did remove that error, thank you. Indeed, there is a large number of atoms with identical cgnr, no idea why. Does it have to do with the order of atoms in your PDB?
On Thu, Apr 2, 2015 at 10:22 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 4/1/15 7:42 PM, Alex wrote: > >> 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: >> > > No, that magnitude of charge is not actually a problem. > > 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. >> >> > The cgnr column will tell you what's going on. Charge groups are > irrelevant if using the Verlet cutoff scheme. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > 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 gmx-users-requ...@gromacs.org. > -- 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 gmx-users-requ...@gromacs.org.