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

[Justin Lemkul]

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
>>
>> ==================================================
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-- 
==================================================

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

==================================================