Hi Gustavo,
This is correct. See also
http://archive.ambermd.org/201010/0503.html
http://archive.ambermd.org/201012/0350.html
All the best,
Andy
On Apr 12, 2011, at 11:05 AM, Gustavo Seabra 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?
>
> 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
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
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--
Dr. Andreas W. Goetz
San Diego Supercomputer Center
Tel : +1-858-822-4771
Email: agoetz.sdsc.edu
Web : www.awgoetz.de
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Received on Tue Apr 12 2011 - 11:30:06 PDT
