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.
> 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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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> 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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Received on Fri Dec 17 2010 - 12:30:03 PST
