Hi,
From the page you sent, it looks like that the 'special bonds' are actually
to define the1–4 interaction scaling factors for LJ and electrostatic terms
(i.e. SCNB and SCEE keywords for amber).
specifically:
special_bonds amber
"The *amber* keyword sets the 3 coefficients to 0.0, 0.0, 0.5 for LJ
interactions and to 0.0, 0.0, 0.8333 for Coulombic interactions, which is
the default for a commonly used version of the AMBER force field, where the
last value is really 5/6. See (Cornell)
<
http://lammps.sandia.gov/doc/special_bonds.html#Cornell> for a description
of the AMBER force field."
So, should you use "special_bonds amber"? I would say "yes" if you've based
your force field on an amber force field. If not, I'm not sure if you get
any help here...
In any case, the answer is probably: try and find out!
You'll want to do some test with your developed force-field parameters
anyway, so you can see what gives 'best' results (closest to some
well-defined experimental or higher-level theory (QM) results).
Just my 2 cents...
Marc
On 12 April 2015 at 11:53, Nahid Khiabani <nahidkhiabani.gmail.com> wrote:
> Actually, I have asked on the LAMMPS mailing list. They said that I should
> ask this question from the force-field developers. This is why I have
> emailed to the Amber maling list.
>
> Thanks,
> Best,
> Nahid
>
> On Sun, Apr 12, 2015 at 3:50 AM, <hannes.loeffler.stfc.ac.uk> wrote:
>
> > I'm not sure why you keep reposting your question but your best bet is
> > probably to ask this on the LAMMPS mailing list.
> > ________________________________________
> > From: Nahid Khiabani [nahidkhiabani.gmail.com]
> > Sent: 12 April 2015 11:33
> > To: amber.ambermd.org
> > Subject: [AMBER] a question for hydrocarbons simulation using amber FF
> >
> > Dear all
> >
> > Hope you are fine.
> >
> > I am using amber FF according to this paper
> > (http://www.ncbi.nlm.nih.gov/pubmed/14531054) also
> > (http://www.ncbi.nlm.nih.gov/pubmed/15116359) to simulate a system
> > including some alkane molecules such as hexane. I am using LAMMPS package
> > to do the simulation.
> >
> > To define an alkane molecule such as hexane I have defined its bonds,
> > angles and dihedrales according to the 2 versions of amber forcefield.
> For
> > non-bonded interactions I also have defined LJ and Columbic pair
> > potentials.
> >
> > I am wondering if I also need to consider
> > special_bonds(http://lammps.sandia.gov/doc/special_bonds.html) for this
> > type of molecules?
> >
> > Thanks a lot for your attention,
> > Best Regards,
> > Nahid
> >
> >
> >
> > --
> > Thanks a lot for your attention,
> > Best Regards,
> > Nahid
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Thanks a lot for your attention,
> Best Regards,
> Nahid
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sun Apr 12 2015 - 04:30:02 PDT
