[gmx-users] Problems about sigma & epsilon to C6 & C12
janne.hirvi at joensuu.fi
Mon Jul 16 09:35:43 CEST 2007
Could you please help me to understand solution as well? I just plotted these
functions so that I combined sigma and epsilon values using rule 3
and corresponding C6 (4*epsilon*sigma^6) and C12 (4*epsilon*sigma^12) values
using rule 1
and got identical plots. What I have missed?
> My problem has solved. Finally I realized that my calculation is wrong.
> Thank you so much!
> On 7/15/07, james zhang <james.zhangj at gmail.com> wrote:
> > From equation 5.3 page 88, I think rule 1 and 3 are equivalent if you
> > convert the parameters.
> > I am sorry. What's the different between rule 1 and 3?
> > I think C6/C12 are used in rule 1 and sigma/epsilon are used in rule 3.
> > But if you convert sigma/epsilon to C6/C12, these two should be
> > I am confused. Can I convert sigma/epsilon to C6/C12 if I want to use gmx
> > force field instead of OPLS ?
> > Thanks.
> > On 7/15/07, David van der Spoel < spoel at xray.bmc.uu.se> wrote:
> > >
> > > james zhang wrote:
> > > > I used rule 3 for ffopls rule 1 for ffgmx.
> > > >
> > > please read the manual.these combination rules are not equivalent.
> > >
> > > there is also combination rule 2, see 5.3.3
> > > --
> > > David.
> > > ________________________________________________________________________
> > >
> > > David van der Spoel, PhD, Assoc. 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://folding.bmc.uu.se
> > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > >
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