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

[Albert Sun]

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?

If input C6 and C12 as in ffgmanb.itp, the potentail energy output is negative, which is not correct!  is it?
 
 
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
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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