[gmx-users] C6 and C12 in ffgmxnb.itp

[David]

On Wed, 2003-12-10 at 19:15, Albert Sun wrote:
> Does the equation (5.1) (page 90 in manual) link C6, C12 with epsilon
> and sigma?   
>  
> should we input C6 and  C12 in .top file  or  epsilon and sigma?
> 
you can do one or the other, but not mix the two. It is determined by
the first section [ defaults ] how the numbers are interpreted. In
ffoplsaanb.itp you will see that it is sigma and epsilon.


> If input C6 and C12 as in ffgmanb.itp, the potentail energy output is
> negative, which is not correct!  is it?
yes, it should have a minimum.
>  
>  
> Many thanks!
>  
> David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>         On Wed, 2003-12-10 at 17:15, Albert Sun wrote:
>         > Dear Users,
>         > 
>         > I used parameters of C6 and C12 in ffgmxnb.itp to compute
>         potential,
>         > the results are all negative, this looks incorrect.
>         > 
>         > In ffgmxnb.itp file, for example C-C nonbond, C6=
>         0.0023402KJ/mol, 
>         > 
>         > C12 = 0.33740E-05 nm.
>         > 
>         you are mixing this stuff up with sigma and epsilon ntoation.
>         see manual
>         
>         
>         > But in other literatures, some researchers used C6 is about
>         0.
>         > 5KJ/mol and C12 is about 0.4nm, this will get positive
>         potential.
>         > 
>         > Do you think the parameters in ffgmxnb.itp is correct?
>         > 
>         > Thanks for your advice.
>         > 
>         > Albert
>         > 
>         > 
>         > 
>         > 
>         > 
>         >
>         ______________________________________________________________________
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>         David.
>         ________________________________________________________________________
>         David van der Spoel, PhD, Assist. Prof., Molecular Biophysics
>         group,
>         Dept. of Cell and Molecular Biology, Uppsala University.
>         Husargatan 3, Box 596, 75124 Uppsala, Sweden
>         phone: 46 18 471 4205 fax: 46 18 511 755
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David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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