[gmx-users] RE: RE: [nonbond_params] section , choice of parameters

[Amir Marcovitz]

Many Thanks Ehud!

I was certainly not aware of that and I'll check it now..

Amir

On Wed, Jul 28, 2010 at 6:22 PM, Ehud Schreiber <schreib at compugen.co.il>wrote:

>  Hi again,
>
>
>
> Yes, you can simply specify sigma and epsilon, but indeed in your case you
> do not want to do so but rather to specify C_6 and C_{12} with the former
> being zero to avoid attraction.
>
> Your .top file should include a [ defaults ] section, perhaps through an
> #include of a .itp file. Perhaps yours is in ffamber99.itp (I don’t have it
> installed so I can’t tell). In this section there are 5 parameters; the
> second is a “combination rule” which must equal 1 for the two numbers to
> represent indeed C_6 and C_{12} (see table 5.3, eq. 5.1-5.4, and in page
> 112).
>
> In short, check whether the second parameter in the [ defaults ] section of
> ffamber99.itp is 1, if not that’s probably the problem. Of course, if you
> change this you’ll screw up all the other parameters, so it seems you could
> either change the force field or create your copy of the files with all the
> relevant LJ parameters changed to the “combination rule”=1 convention.
>
>
>
>
>
> *From:* Ehud Schreiber
> *Sent:* Wednesday, July 28, 2010 3:01 PM
> *To:* 'gmx-users at gromacs.org'
> *Subject:* RE: [nonbond_params] section , choice of parameters
>
>
>
> Hi Amir,
>
>
>
> Are you sure you’re giving the parameters indeed as C_6 and C_{12}?
>
> According to the combination rule in the [ defaults ] section, you may be
> giving the two parameters directly as sigma and epsilon; sigma=0 (as well as
> epsilon=0) would give an identically zero potential . See sections 5.3.3 and
> 5.7.1 in the manual (version 4.0).
>
>
>
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