Hi Marc
Thanks a lot for your effective comment.
I modified the 3 coefficients to 0.0, 0.0, 0.5 for LJ interactions and to
0.0, 0.0, 0.8333 for Coulombic interactions to some other values. According
the amber FF parameters and my modified coefficients I have more accurate
results in comparison with experimental data rather than the above common
values. So, I am wondering if I can use the modified values for the
coefficients?
Thanks a lot,
Best Regards,
Nahid
On Sun, Apr 12, 2015 at 4:12 AM, Marc van der Kamp <marcvanderkamp.gmail.com
> wrote:
> 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Thanks a lot for your attention,
Best Regards,
Nahid
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Received on Sun Apr 12 2015 - 05:00:02 PDT
