[gmx-users] Non-bonded parameters in Gromacs

[Anton Feenstra]

Marc Baaden wrote:
> 
> feenstra at chem.vu.nl said:
> >> > the FudgeLJ and FudgeQQ parameters do ?? [..]
> >> What they say they do on page 98.
> 
> Sorry, but I still am not fully convinced. Are they multiplicative
> factors or divisions ? Eg to get 1/2 interactions, do I need to set
> them to 0.5 or to 2.0 ?

I think  they are muliplication factors (that would make most sense),
but I am not sure...

> feenstra at chem.vu.nl said:
> >> I've posted a rudimentary topology parsing script to the list [..]
> 
> Yes. I have tried it. But it's more for monitoring purposes I guess ?
> I mean, grompp would not read that file as a topology, would it ?

I think it actually would, but I don't remember having tried it.
The .top file format supports optional explicit parameters everywhere,
so I don't see a problem in principle and it would probably be trivial
to fix any possible problems. I hope you can read my script, if not 
you can send me a 'bug-report' and I'll fix it for you.


-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
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