Ah, now I see, thanks. Yes, this entirely follows the paradigm of biomolecules. I still insist that Gromacs was a better choice for my project than LAMMPS. :)
On Thu, Apr 2, 2015 at 12:31 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 4/2/15 2:28 PM, Alex wrote: > >> 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? >> >> > No, it has to do with the definition of a charge group. In the x2top.c > function set_cgnr(), the charge group index is only incremented once an > integral charge has been accumulated, per convention. Probably in your > case, it takes a lot of atoms before that criterion is satisfied. > > -Justin > > > 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. >>> >>> > -- > ================================================== > > 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.