[gmx-users] gen-pairs

[Justin Lemkul]

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

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