[gmx-users] Re: #include "ffXXX.itp"

[Chih-Ying Lin]

Hi
>From Justin:
 " Yes, as long as those atoms are listed as bonded within the [ bonds ]
 section of your .top file. "

The specific "bonded function", such as gb_28",  should be also listed
on the [bonds] section, right?

Or, it could assign NOTHING for me, right?

so,
[bonds]
; ai  aj  funct
8     9     gb_28
is correct.......


[bonds]
; ai  aj  funct
8     9
is INCORECT.......  and 8 , 9 will NOT be automatically bonded,  right?

The same for the nonbonded parts, right?
Thank you
Lin








On 9/22/08, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
>  Chih-Ying Lin wrote:
>
> > HI
> >
> >  The command
> >  #include "ffXXX.itp" is putting in the .top file.
> >
> >  How does this command automatically assign the force field
> >  parameters which I did not assign in my .top file?
> >
> >  Is it based on the atom types which I assign in my .top file?
> >  Then, all the force field parameters from "include ffXXX.itp"  will
> > give the both bonded
> >  and non-bonded parameters according the atom types, right?
> >
> >
> > I mean...... once I determine the atom type.......such as NL and CH3......
> > there is a bond between NL and CH3.....
> > But i did not assign the bond parameters in my .top file while I add
> > the command
> > "#include "ffXXX.itp" in my .top file.
> >
> > Will this command #include "ffXXX.itp" automatically assign a bond
> > parameter for it?
> >
> >
> >
>
>  Yes, as long as those atoms are listed as bonded within the [ bonds ]
> section of your .top file.
>
>
> >
> > Other than this, there are so many non-bonded force field parameters.
> > Once, I determine the atom types such as O and CR1.
> > But, I did not assign any non-bonded parameters for them in my .top file.
> > Will this command  #include "ffXXX.itp" assign all the non-bonded
> > force field parameters for me based on the atom types automatically?
> >
> >
>
>  Yes.
>
>  -Justin
>
>
> >
> > Thank you
> > Lin
> >
> >
>
>  --
>  ========================================
>
>  Justin A. Lemkul
>  Graduate Research Assistant
>  Department of Biochemistry
>  Virginia Tech
>  Blacksburg, VA
>  jalemkul[at]vt.edu | (540) 231-9080
>  http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>  ========================================
>