[gmx-users] gen-pairs

[Alexander Alexander]

I have this system in two different states, and I am interested in the
difference between total energy of these states, I found out that the
result changes when gen-pairs is YES and NO.

I mean [ \delta(S1(tot-ene)-S2(tot-ene))(NO) ] is not the same as [
\delta(S1(tot-ene)-S2(tot-ene))(YES) ] !?

Regards,
Alex

On Fri, Jun 3, 2016 at 11:59 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/3/16 5:58 PM, Alexander Alexander wrote:
>
>> 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?
>>
>>
> Yes, it's completely irrelevant.
>
> -Justin
>
>
> 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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>>
> --
> ==================================================
>
> 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
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