[gmx-users] combination rules -- the part about the combinationrules

[Mark Abraham]

Shuangxing Dai wrote:
> Thanks for your answer. I changed the non-bond parameters in 
> ffgmxnb.itp.  like
> ; i    j   func     a        b    c6
> Zn  O        2     ...     .....   .... 
> But error occured..
> 
>  
> 
> ERROR 1 [file ffgmxnb.itp, line 270]:
> 
>   Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
> 
>  
> 
>  
> 
> ERROR 2 [file ffgmxnb.itp, line 271]:
> 
>   Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
> 
>  
> 
>  
> 
> ERROR 3 [file ffgmxnb.itp, line 272]:
> 
>   Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
> 
>  
> 
> I think I have indicated that the function type is 2 (means Buckingham). 
> Anything else need to do with this ?

... specify that the default nonbonded type is not LJ? Have a look in 
Chapter 5 of the manual.

> Also, I want to fix some atoms in the boundary and specify displacement 
> to some atoms, anayone knows how to do this?

You can freeze groups of atoms, or use position restraints, or pull 
groups of atoms, but you should look first in the manual for the 
information that is there.

Mark