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?
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
>> > > _______________________________________________
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>> > > 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
>> >
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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 - 11:30:03 PDT
