On Mon, Dec 9, 2013 at 3:05 PM, Ehsan Sadeghi <es...@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

jalem...@outerbanks.umaryland.edu | (410) 706-7441


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