[gmx-users] gen-pairs

[Alexander Alexander]

Many thanks for your response.

So, do you mean that the "gen-pairs" can be freely NO or YES for this
system with no change in any of the results?

The best,
Alex

On Fri, Jun 3, 2016 at 11:03 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/3/16 8:49 AM, Alexander Alexander wrote:
>
>> Dear Gromacs user,
>>
>> Surprisingly I am wondering why I have no warning while I assigned "NO"
>> for
>> the "gen-pairs" in [ default ] section of my .top file, although I have no
>> pair type neither in my .top file nor in ffnonbonded.itp for these atoms?
>>
>>
> Pairs are 1-4 (intramolecular) interactions.  You have two atom types that
> are not bonded, so there are no pair interactions.
>
> -Justin
>
>
> I am referring to this statement in gromacs-manual: "When gen-pairs is set
>> to “no,” grompp will give a warning for each pair type for which no
>> parameters are given".
>>
>> My system is a pure transition metal solid that it's topol file comes
>> below:
>>
>> topol.top
>> -------------------------
>> ; topol file for A3B
>> ; force field parameters in below
>> [ Defaults ]
>> ;  nbfunc        comb-rule       gen-pairs       fudgeLJ  fudgeQQ
>>      1                   3                         no
>> 0.5       0.5
>>
>> [ atomtypes ]
>> ;   name      mass        charge    ptype       sigma           epsilon
>>      A            32.00          0.21          A        2.27357e-01
>> 25.1
>>      B            6.700         -0.63          A        1.714534e-01
>> 4.4
>>
>> [ moleculetype ]
>> ; Name            nrexcl
>>   A                       1
>> [ atoms ]
>> ;  nr     at type  resnr   residue   atom name   cgnr     charge
>>  mass
>>    1            A         1          A                   A
>> 1       0.21           32.00
>>
>> [ position_restraints ]
>> ; ai  funct  fcx    fcy    fcz
>>    1    1    2000   2000   2000
>>
>> [ moleculetype ]
>> ; Name            nrexcl
>>   B               1
>> [ atoms ]
>> ;  nr     at type  resnr   residue   atom name   cgnr     charge
>>  mass
>>    1                              B        1          B          B
>> 1      -0.630         6.70
>>
>> [ position_restraints ]
>> ; ai  funct  fcx    fcy    fcz
>>    1    1    2000   2000   2000
>>
>> [ system ]
>> ; Name
>>    A3B
>>
>> [ molecules ]
>> ;mol_name number
>>    A    14400
>>    B     4800
>> -----------------------------------------------------
>>
>>
> --
> ==================================================
>
> 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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