[gmx-users] combination rules -- the part aboutthecombinationrules

Mark Abraham Mark.Abraham at anu.edu.au
Wed Mar 4 07:00:18 CET 2009

Shuangxing Dai wrote:
> Thank you for your help. I checked all the force field, all of them are 
> with default non-bond params in LJ. So I still need to try new solution.
> I add my non bond parameters in the .top file generated. Force field 
> files were not changed. Then I use grompp, the error was:

That wasn't the question. Do you *need* the rest of the force field? If 
you're only doing ZnO then you don't need the rest. IIRC you've never 
told us what you're trying to simulate, which tends to frustrate any 
effort to help you.

> '[ nonbond_params ]'
> Invalid order for directive nonbond_params

Yep, these can't appear anywhere after a [molecule] directive. See 
chapter 5 of the manual.

> Rather confused by setting up Buckingham potential parameters...

Make sure you read the advice you're being given:

>     If you need other atoms as well, you will need to find
>     a consistent force field, probably or completely LJ
>     or completely Buckingham.


>      > No, because it's not a reasonable goal. Your new atomtypes are
>     talking a
>      > different vdW "language". That doesn't work.

>      > > And what
>      > > force field to choose if not ffgmx?
>      >
>      > That's your homework I'm afraid. You'll have to read the literature.



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