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

Justin A. Lemkul jalemkul at vt.edu
Mon Sep 22 19:39:16 CEST 2008

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?



> Thank you
> Lin


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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