[gmx-users] gen-pairs
Alexander Alexander
alexanderwien2k at gmail.com
Sat Jun 4 00:40:54 CEST 2016
Thanks, although, each of them is a 2 ns NVT calculation, not a
single-point energy.
By the way, then why does "gmx grompp" shows below when gen-pairs is yes if
no pair is present?
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
>>>
>>> ==================================================
>>> --
>>> 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
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