[gmx-users] The largest charge group contains [GIANT CRAPTON] of atoms
nedomacho at gmail.com
Thu Apr 2 20:28:17 CEST 2015
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 <jalemkul at 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 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
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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