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

[Alex]

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 <jalemkul at 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 <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
>>>
>>> --
>>> ==================================================
>>>
>>> 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
>>> 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-request at 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
>
> jalemkul at 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-request at gromacs.org.
>