Dear Andreas, dear Jason!
Thank you for well-founded explanation!
On Sat, Dec 18, 2010 at 5:02 AM, Jason Swails <jason.swails.gmail.com> wrote:
> Hello,
>
> My comments are below:
>
> On Fri, Dec 17, 2010 at 3:01 PM, Andreas Goetz <agoetz.sdsc.edu> wrote:
>
>> Dear Dmitry,
>>
>> while it is true that total energies are irrelevant and only relative
>> energies have significance, you should always use the total energy from the
>> Amber output (Etot) to obtain relative energies, otherwise you would be
>> using an energy expression that is not clearly defined.
>>
>> Now, if I understand correctly, the question you are posing is geared
>> towards a different problem, which is how to deal with the noise on reaction
>> path energies that is due to conformational changes in the environment. This
>> is not directly related to QM/MM but also holds for pure QM or pure MM
>> calculation. You probably have to do something like umbrella sampling along
>> the reaction path. Maybe someone with more experience can comment on this.
>>
>> I hope this helps.
>>
>> All the best,
>> Andy
>>
>> On Dec 17, 2010, at 4:31 AM, Dmitry Nilov wrote:
>>
>> > Dear Ross, dear Andreas! Could you be so kind to answer my question
>> > associated with the topic!
>> > As I suppose, it is not relevant to use TOTAL potential energy of
>> > complex protein-solvent QM/MM system (where QM is the active site) to
>> > compare two different energy states of the active site, because
>> > motions in regions distant to the active site may significantly affect
>> > the energy profile.
>>
>
> You are right in that distant motions may have a large impact on your
> potential energy. I would disagree that you should only consider the SCF
> energy, though, since as Andreas pointed out, any 'partial energy' term is
> not well-defined. This is because the potential terms are non-orthogonal
> (they all depend on each other). In fact, the ESCF depends on the distant
> conformations as well inasmuch as they change the electric field felt at the
> various positions in the quantum region.
>
> For this reason, you can only really consider the total potential energy
> when comparing two states. However, for flexible molecules, potential
> energy is strongly conformation dependent and this "noise" is a fact of
> life. What you have to do is average over these conformations in a
> statistical mechanically correct way, which is to say you have to sample
> from the appropriate boltzmann distribution. Thus, if you want to find the
> free energy along a reaction pathway, you will average over all other
> degrees of freedom by building a proper ensemble at each point along the
> path (you can use either monte carlo or molecular dynamics for this). This
> is called a potential of mean force (PMF), and can be obtained, as Andreas
> suggested, with umbrella sampling, though other methods can be used as well.
>
> Hope this helps,
> Jason
>
>> So, is it reasonable in this case to use just DFTBESCF energies to
>> > reconstruct the energy (enthalpy) profile of a reaction while QM-MM
>> > VDWAALS energies are not included in DFTBESCF?
>> >
>> > On Fri, Dec 17, 2010 at 1:18 AM, Andreas Goetz <agoetz.sdsc.edu> wrote:
>> >> Dear Markus,
>> >>
>> >> The answer to all your questions below is 'yes'. You got everything
>> right.
>> >> Ross will send a more detailed email for anybody that didn't understand
>> it so far.
>> >>
>> >> All the best,
>> >> Andy
>> >>
>> >> For reference the links to earlier posts:
>> >> http://archive.ambermd.org/201010/0503.html
>> >> http://archive.ambermd.org/201011/0098.html
>> >>
>> >> On Dec 16, 2010, at 7:49 AM, Markus Kaukonen wrote:
>> >>
>> >>> Dear Amber,
>> >>>
>> >>> This issue has already been dealt with on this list, but I did not
>> >>> quite get it, so here we go again:
>> >>>
>> >>> In QM/MM calculation with DFTB as QM engine one gets output like (with
>> Amber10)
>> >>>
>> >>> NSTEP ENERGY RMS GMAX NAME NUMBER
>> >>> 1 -2.1816E+04 1.7957E+01 1.4342E+02 C36 12502
>> >>>
>> >>> BOND = 2156.1278 ANGLE = 6029.2390 DIHED =
>> 9228.7109
>> >>> VDWAALS = -7560.4126 EEL = -52399.6187 EGB =
>> -5475.9033
>> >>> 1-4 VDW = 2123.9140 1-4 EEL = 37427.0797 RESTRAINT =
>> 0.0000
>> >>> DFTBESCF= -13345.6223
>> >>>
>> >>> Question: What is included in the term 'DFTBESCF'
>> >>> Is it only the QM energy of the QM region (terminated with H atoms)
>> >>> and electrostatic interaction of QM nuclei and electron cloud with
>> >>> unscaled point charges of the MM region?
>> >>>
>> >>> Vdw interaction between QM and MM region is in included into 'VDWAALS'
>> >>> and '1-4 VDW' ?
>> >>> Possible bond, angle and dihedral terms between QM and MM regions are
>> >>> included into the classical terms (BOND, ANGLE, DIHED)?
>> >>> Solvation energy of QM region is in included into EGB ?
>> >>>
>> >>> Did I get it right?
>> >>>
>> >>> terveisin, Markus
>> >>
>> >> --
>> >> 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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>> >>
>> >
>> >
>> >
>> > --
>> > Dmitry Nilov,
>> > Lomonosov Moscow State University
>> >
>> > _______________________________________________
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>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>> --
>> 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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>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
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>
--
Dmitry Nilov,
Lomonosov Moscow State University
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Received on Sat Dec 18 2010 - 01:00:03 PST
