[gmx-users] gen-pairs

[Justin Lemkul]

On 6/3/16 6:40 PM, Alexander Alexander wrote:
> Thanks, although, each of them is a 2 ns NVT calculation, not a
> single-point energy.
>

Then the comparison, in the context of the effect of gen-pairs, is useless.

> By the way, then why does "gmx grompp" shows below when gen-pairs is yes if
> no pair is present?
>

Because you're telling it to by setting it to "yes" - there is no [pairtypes] 
entry for a given combination of atom types, so grompp generates it.  Whether or 
not it's actually used for the simulation is a different question.  In your 
case, pairs can be generated or not, and in neither case will they actually be 
used in the simulation.

-Justin

> Generating 1-4 interactions: fudge = 0.5
> Generated 3 of the 3 1-4 parameter combinations
>
> Best regards,
> Alex
>
> On Sat, Jun 4, 2016 at 12:20 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 6/3/16 6:14 PM, Alexander Alexander wrote:
>>
>>> 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) ] !?
>>>
>>>
>> That's not a definitive test.  If you do a single-point energy evaluation
>> of a given set of coordinates with gen-pairs set to "no" and "yes" and get
>> a different answer, something is wrong.  Your topology shows no bonds,
>> therefore there can be no 1-4, therefore no pairs.  Pairs are what
>> gen-pairs affects.
>>
>> -Justin
>>
>>
>> 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
>>>>>>
>>>>>> ==================================================
>>>>>> --
>>>>>> Gromacs Users mailing list
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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
>>>>
>>>> ==================================================
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>>>> Gromacs Users mailing list
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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
>>
>> * Please search the archive at
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>>
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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

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