[gmx-users] Buckingham interactions

[Mark Abraham]

On 31/08/2011 2:18 AM, xiaojing gong wrote:
> Dear all
>   I want to use Buckingham interactions. And I read the manual, but I 
> still have some questions for asking:
>         1 ) I need to write the BN  Buckingham interactions in the 
> format of GMX. see the following:
>        Buckingham    a(ev)  b(nm)  C(ev nm^6)
>         B-B                 6260 0.1 0
>         B-N 33 0.7 0
>         N-N 4300 0.12 0
>
>            where shall I put the [defaults] lines, could I put these 
> in mydefined.itp file?

You can't put these in a molecule .itp file. These lines go in the 
forcefield.itp file that is #included at the beginning of normal .top 
files. There can only be one [defaults] in your whole .top, including 
the #included files.

>
>            [ defaults ]
>  ; nbfunc   comb-rule   gen-pairs  fudgeLJ  fudgeQQ
>      2        1           no         1.0      1.0
>
>        2) There are three parameters for Buckingham interactions, can 
> I write as in the following way?
>
>          [ atomtypes ]
> ;type    mass    charge   ptype    a          b      C6
>  B      30.07     1.15         A ?? ?? ??
>  N      14.01    -1.15        A  ?? ?? ??
>

Sure. What's the alternative?

> 3) The given Buckingham interaction parameter of B-N may not obey any 
> combine rules provided in GMX, what shall I do?

You need to provide suitable [nonbond_params] lines. See manual section 
5.3.2

Mark

>
> I will be appreciate it if you can give me some suggestions!
>
> XJ
>
>

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