[gmx-users] OPLS force field issue

[Justin Lemkul]

On Mon, Dec 9, 2013 at 3:05 PM, Ehsan Sadeghi <esa38 at sfu.ca> wrote:

> Thanks Justin.
>
> I added the bond description in the ffbonded.itp but it does not show in
> the topol.top file.
>
> In ffbonded.itp we have:
>
> [ bondtypes ]
> ; i    j  func       b0          kb
>   OW    HW      1    0.09572   502080.0   ; For TIP4F Water - wlj 1/98
>   OW    LP      1    0.01750   753120.0   ;          -idem-
>   C*    HC      1    0.10800   284512.0   ;
>   C1    C2       1    0.16020   292880.0   ;
>   C2    C3       1    0.16020   292880.0   ;
>
> " I am not sure to put C   C or C1   C2 here; I tried both, neither
> worked."
>
> [ angletypes ]
> ;  i    j    k  func       th0       cth
>   HW     OW     HW      1   109.500    627.600   ; For TIP4F Water - wj
> 1/98
>   HW     OW     LP      1    54.750    418.400   ; For TIP4F Water - wj
> 1/98
>   OU     U      OU      1   180.000   1255.200   ; J Phys Chem 97, 5685
> (1993)
>   HC     C*     CW      1   126.800    292.880   ;
>   HC     C*     CB      1   126.800    292.880   ;
>   HC     CS     CW      1   126.800    292.880   ;
>
> ----------------
> However, the parameters that we had in topol file are different:
>
> [ bonds ]
> ;  ai    aj funct            c0            c1            c2            c3
>     1     2     1
>     1     5     1
>
> [ angles ]
> ;  ai    aj    ak funct            c0            c1            c2
>    c3
>     2     1     5     1
>     2     1     6     1
>     5     1     6     1
> --------------------------------
>
> How gromacs can find c0, c1,c2 and c3 from b0, kb, th0, and cth in the
> ffbonded.itp?
>
>
It looks them up from ffbonded.itp.  You have a bond between atoms 1 and
2.  Atoms 1 and 2 have assigned types, per the [atoms] directive.  grompp
goes into ffbonded.itp and looks for a bond between the types corresponding
to that set of atoms.

-Justin

-- 

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

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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