On Tue, Apr 12, 2011 at 11:05 AM, Gustavo Seabra
<gustavo.seabra.gmail.com>wrote:
> Hi Jason,
>
> I may be wrong (and I often am), but I'm under the impression that the
> VDW terms including QM and MM atoms are included in the classical VDW
> energy, *not* in the SCF energy (ESCF). AFAIK, the SCF energy includes
> only the energy from the SCF itself, which includes the interaction
> with the point charges because the SCF is done in the presence of
> those. Is that not correct?
>
That's correct (you would know better than me, anyway ;) ), I just thought
Jurica wanted to avoid calculating those terms altogether, not just have
them *not* included in the ESCF total. Sorry, I was answering the question
I thought was asked, but it's not so clear what was initially asked for...
(I hadn't thought about your interpretation)
Jurica -- if you want to avoid calculating any QM-MM non-bonded interaction
terms altogether, you'll need to take my suggestion. If you just want to
make sure that it's not included in ESCF, then Gustavo is right and it's
included as part of the classical VDWAALS term, anyway.
All the best,
Jason
>
> Gustavo Seabra
> Professor Adjunto
> Departamento de Química Fundamental
> Universidade Federal de Pernambuco
> Fone: +55-81-2126-7417
>
>
>
> On Tue, Apr 12, 2011 at 12:00 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
> > Hello,
> >
> > The solvent bonded terms will necessarily be zero, since there is *no*
> > dihedral parameter, and if it's a rigid water molecule, then SHAKE holds
> the
> > bonds at their fixed, equilibrium distance.
> >
> > On to the non-bonded interactions. As long as the water Oxygen still has
> a
> > VDW radius, it will calculate the VDW interaction between the MM and QM
> > atoms (HWs have no VDW radii). Squashing those VDW terms could be
> tricky,
> > depending on what, exactly, you're trying to do.
> >
> > Do you care if the water molecules experience inter-molecular VDW forces?
> > Or do you want to get rid of *ALL* other non-bonded interactions (such as
> > MM-MM VDW interactions)?
> >
> > If you want to get rid of all VDW interactions, then you'll have to
> create
> > an frcmod file like previously suggested, and set the OW atom type to
> have 0
> > VDW radius/well-depth. Have a look in http://ambermd.org/formats.html,
> > along with the ambertools manual to find out how to format an frcmod
> file.
> >
> > However, if all you want to do is zero out the VDW interactions between
> QM
> > and MM atoms, then that's a bit trickier. You have to figure out how the
> > LENNARD_JONES_ACOEF and LENNARD_JONES_BCOEF are indexed (by atom type,
> > etc.), and zero out ONLY those terms that represent QM atom types
> > interacting with MM atom types.
> >
> > One last piece of advice: I would NOT change that water atom types, since
> > those are hard-coded in places in the code to recognize rigid waters; so
> you
> > don't want to get rid of that.
> >
> > Hope this helps,
> > Jason
> >
> > On Tue, Apr 12, 2011 at 7:13 AM, Jurica Novak <jnovak.irb.hr> wrote:
> >
> >> Great! If in Amber's mechanical embedding QM/MM approach reported SCF
> >> energy
> >> includes *only* electrostatic influence of "non-QM" atoms on "QM" atoms
> >> (with Ewald summation included and all bonded and non-bonded
> contributions
> >> of "non-QM" atoms are exactly zero), that would be perfect. Does anyone
> >> know
> >> which flag(s) should be turned on for a such single point run
> >> ('independent'
> >> of Amber's QM/MM dynamics)?
> >>
> >> In case of using "NTR" keyword there is additional contribution to
> total
> >> energy - RESTRAINT. Another option that I've tried is using *"ibelly*"
> >> mask,
> >> allowing only "QM" atoms to move. This helped in sense that all bonded
> >> contributions of solvent molecules are exactly zero (I've compared
> bonded
> >> contributions to energy by comparing calculations with *"ibelly*"
> keyword
> >> on
> >> and only "QM" subsystem in gas phase). But, non-bonding interactions of
> >> "non-QM" atoms remain sofar as unsolved problem to me.
> >>
> >> Best regards,
> >> Jura
> >>
> >> 2011/4/12 Gustavo Seabra <gustavo.seabra.gmail.com>
> >>
> >> > Could you describe in more detail what you want to do?
> >> >
> >> > In Amber's QM/MM approach, when you do a single point calculation, the
> >> > SCF energy reported already includes the influence of "non-QM" atoms
> >> > as point charges over the QM region. If you also turn off the periodic
> >> > boundary conditions, that's all you get. Otherwise, an Ewald sum for
> >> > the long range electrostatic interactions will also br included.
> >> > Finally, you can look at the "NTR" and "NTF" options for sander to
> >> > turn off particular terms of the force field.
> >> >
> >> > HTH,
> >> > Gustavo.
> >> >
> >> > On Tuesday, April 12, 2011, Jurica Novak <jnovak.irb.hr> wrote:
> >> > > Dear Amber user,
> >> > >
> >> > > Could anyone suggest me how to run Amber single point calculation in
> a
> >> > way
> >> > > that atoms of solvent are represented only as a point charges (with
> all
> >> > > other interactions - bonding and nonbonding - turned off), while in
> the
> >> > same
> >> > > time all interactions of solute atoms are accounted for?
> >> > >
> >> > > Thanks in advance,
> >> > >
> >> > > Jura
> >> > > _______________________________________________
> >> > > AMBER mailing list
> >> > > AMBER.ambermd.org
> >> > > http://lists.ambermd.org/mailman/listinfo/amber
> >> > >
> >> >
> >> > --
> >> > Gustavo Seabra
> >> > Professor Adjunto
> >> > Departamento de Química Fundamental
> >> > Universidade Federal de Pernambuco
> >> > Fone: +55-81-2126-7417
> >> >
> >> > _______________________________________________
> >> > 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
> >>
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Apr 12 2011 - 11:30:05 PDT
