The energy of the whole system in a QMMM simulation
jts2t... at gmail.com
jts2t... at gmail.com
Mon Sep 11 11:28:09 UTC 2017
Thanks for your patience , Jadzia !
Your answer have solved a problem for me. My major is computational
mathematics.
If we want to prove the superiority of QMMM model over MM model in this
simulation, what is the sensible quantity ? The oscillation of the energy ?
Or the dos of the system ? What quantity should taken to compare ?
在 2017年9月11日星期一 UTC+8下午2:53:39，Jadzia写道：
>
> The reference point of the absolute potential energy can usually be chosen
> arbitrary, and the absolute potential energy itself is therefore usually
> meaningless. See for instance:
>
> -
> https://www.quora.com/Why-do-we-need-a-reference-point-to-determine-potential-energy
> - http://hyperphysics.phy-astr.gsu.edu/hbase/pegrav.html
> - https://en.wikipedia.org/wiki/Potential_energy#Reference_level
>
> What is meaningful and used in most calculations are energy differences.
> And here the choice of the reference point does not matter because it
> cancels out in the substraction.
>
> If you have the same system, and use at at first one layer of QM atoms and
> then two layers of QM atoms, then you are using two different molecular
> models for your system, even if the MM and the QM models are the same. The
> potential energy reference point will change, since some atoms are treated
> with another method which has a difference reference point.
>
> Best wishes,
> Jadzia
>
>
>
> On Monday, September 11, 2017 at 7:59:06 AM UTC+2, jts2... at gmail.com
> wrote:
>>
>> Hi Jadzia,
>>
>> I don't major in physical or chemistry, so what you have suggested
>> confused me for a long time. My example comes from the following page:
>> https://www.cp2k.org/exercises:2017_ethz_mmm:qmmm
>> <https://www.google.com/url?q=https%3A%2F%2Fwww.cp2k.org%2Fexercises%3A2017_ethz_mmm%3Aqmmm&sa=D&sntz=1&usg=AFQjCNGiF0gJ6mRlaGSe7--tVuWgLftgjA>
>> .
>>
>> The simulation uses the same molecular model (as far as I know, it's
>> true) for the MM region (I use the same potential function through 1-layer
>> simulation and 2-layer simulation and more). Does it mean the model can
>> compare now ?
>>
>> Besides, the energy of the 1-layer and 2-layer and even more-layer
>> simulation is nearly geometric series. If energy of 1-layer is 1, then
>> the energy of 2-layer is almost 2, and 3 of 3-layer. It makes me consider
>> the energy belongs to the QM region. Hence, I want to know how to calculate
>> the whole energy of the system.
>>
>> Or the geometric series is just a coincidence ? There is some mistake in
>> my understanding ?
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> 在 2017年9月11日星期一 UTC+8上午12:19:07，Jadzia写道：
>>>
>>> Hello again,
>>>
>>> in the case that you mean that you are using a different number of QM
>>> atoms, a significant energy difference can be expected. The reason is that
>>> different molecular models assign different energies to the same
>>> atoms/molecules. In particular QM atoms/molecules often have a much lower
>>> energy than MM atoms. QM models for instance usually include the
>>> electron-nuclei interactions explicitly while MM models do not, therefore
>>> you usually cannot directly compare the total energy of different molecular
>>> models even if the system is the same. If you shift the scale properly
>>> between the different models, then a comparison should be possible in
>>> theory, but I have not experience with that.
>>>
>>> Best wishes,
>>> Jadzia
>>>
>>>
>>>
>>> On Sunday, September 10, 2017 at 5:24:40 PM UTC+2, jts2... at gmail.com
>>> wrote:
>>>>
>>>> Hi, Matt, bother you again.
>>>>
>>>> The real problem I want to figure out is, when I set 1-layer QM atoms,
>>>> the energy is
>>>> Total FORCE_EVAL ( QMMM ) energy (a.u.): -351.508815087281562
>>>>
>>>> While I set 2-layer QM-atoms, the energy is
>>>> Total FORCE_EVAL ( QMMM ) energy (a.u.): -696.366434340290539
>>>>
>>>> What bother me is that the energy should be almost the same, but the
>>>> fact is that they differ nearly twice.
>>>> So I want to know if there is some mistake in my understanding, or is
>>>> there some mistake in my setting ?
>>>>
>>>> 在 2017年9月8日星期五 UTC+8下午5:14:30，Matt W写道：
>>>>>
>>>>> The line I suggested _is_ the total energy QM + MM + QM-MM
>>>>>
>>>>> If you set print level medium you should see something like
>>>>>
>>>>> QMMM| Evaluating forces on MM atoms due to the:
>>>>> QMMM| - QM/MM Coupling computed collocating the Gaussian Potential
>>>>> Functions.
>>>>> QMMM| QM/MM Nuclear Electrostatic Potential :
>>>>> -0.210189515
>>>>> QMMM| QMMM Total Energy (QM + QMMM electronic + QMMM nuclear):
>>>>> -694.056114328
>>>>> QMMM| MM energy NOT included in the above term! Check for:
>>>>> FORCE_EVAL ( QMMM )
>>>>> QMMM| that includes both QM, QMMM and MM energy terms!
>>>>>
>>>>> ENERGY| Total FORCE_EVAL ( QMMM ) energy (a.u.):
>>>>> -696.223035107415399
>>>>>
>>>>> Which gives the energy with and without the MM energy - so you can
>>>>> figure out the MM energy.
>>>>>
>>>>>
>>>>> On Friday, September 8, 2017 at 6:45:52 AM UTC+1, jts2... at gmail.com
>>>>> wrote:
>>>>>>
>>>>>> Hi, Matt,
>>>>>> Thanks for your advice!
>>>>>>
>>>>>> I did as you suggest, then I typed in the command 'grep energy
>>>>>> *.out'. But the results said
>>>>>>
>>>>>> QMMM | MM energy NOT included in the above term! Check for:
>>>>>> FORCE_EVAL(QMMM) that includes both QM, QMMM and MM energy terms !
>>>>>>
>>>>>> So I still didn't get the MM energy message.
>>>>>>
>>>>>> As far as my understanding, I should add something else in the &MM
>>>>>> section, maybe an additional &FORCE_EVAL to output the information of MM
>>>>>> region ?
>>>>>> Or there is something important ignored ?
>>>>>>
>>>>>> 在 2017年9月8日星期五 UTC+8上午4:16:40，Matt W写道：
>>>>>>>
>>>>>>> At each step of a geo_opt run you should see something like
>>>>>>>
>>>>>>> ENERGY| Total FORCE_EVAL ( QMMM ) energy (a.u.):
>>>>>>> -696.237954025524573
>>>>>>>
>>>>>>> after all the QS output, that gives you the total energy of the
>>>>>>> system (at least if print_level is medium)
>>>>>>>
>>>>>>> On Thursday, September 7, 2017 at 6:33:03 PM UTC+1, Jadzia wrote:
>>>>>>>>
>>>>>>>> I am not sure if the question is really "where the file is" since
>>>>>>>> it will most likely be nowhere. And to be honest I don't know how to write
>>>>>>>> a similar file for the energies for geo_opt as for MD simulations since
>>>>>>>> only in the MD section there seems to be this print option, which might not
>>>>>>>> be used during geo_opt (not sure about it).
>>>>>>>>
>>>>>>>> But a workaround might be as follows: One can run cp2k with the -o
>>>>>>>> option to store the output of the geometry optimization in a file, and then
>>>>>>>> one could grep the energy out of that file.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On Thursday, September 7, 2017 at 5:05:04 PM UTC+2,
>>>>>>>> jts2... at gmail.com wrote:
>>>>>>>>>
>>>>>>>>> Thanks for your suggestion, which works well in a example in
>>>>>>>>> official website, but fails in another case.
>>>>>>>>>
>>>>>>>>> I run a GEO_OPT simulation using QMMM method, the original
>>>>>>>>> motion.inc is as follows
>>>>>>>>> &MOTION
>>>>>>>>> &GEO_OPT
>>>>>>>>> OPTIMIZER LBFGS
>>>>>>>>> &END
>>>>>>>>> &CONSTRAINT
>>>>>>>>> &FIXED_ATOMS
>>>>>>>>> LIST 1..16
>>>>>>>>> EXCLUDE_MM .TRUE.
>>>>>>>>> EXCLUDE_QM .FALSE.
>>>>>>>>> &END FIXED_ATOMS
>>>>>>>>> &END CONSTRAINT
>>>>>>>>> &END MOTION
>>>>>>>>>
>>>>>>>>> Then I added the MD section, they became
>>>>>>>>> &MOTION
>>>>>>>>> &GEO_OPT
>>>>>>>>> OPTIMIZER LBFGS
>>>>>>>>> &END
>>>>>>>>> &CONSTRAINT
>>>>>>>>> &FIXED_ATOMS
>>>>>>>>> LIST 1..16
>>>>>>>>> EXCLUDE_MM .TRUE.
>>>>>>>>> EXCLUDE_QM .FALSE.
>>>>>>>>> &END FIXED_ATOMS
>>>>>>>>> &END CONSTRAINT
>>>>>>>>> &MD
>>>>>>>>> &PRINT
>>>>>>>>> &ENERGY
>>>>>>>>> FILENAME=total.ener
>>>>>>>>> &EACH
>>>>>>>>> GEO_OPT 1
>>>>>>>>> &END EACH
>>>>>>>>> &END ENERGY
>>>>>>>>> &END PRINT
>>>>>>>>> &END MD
>>>>>>>>> &END MOTION
>>>>>>>>>
>>>>>>>>> The strange thing is that there wasn't any file named *total.ener*
>>>>>>>>> in the current directory. Where is the question ?
>>>>>>>>> The &EACH section is not correct ?
>>>>>>>>>
>>>>>>>>> Expect for your kind reply !
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> 在 2017年9月7日星期四 UTC+8下午12:13:16，Jadzia写道：
>>>>>>>>>>
>>>>>>>>>> Hello,
>>>>>>>>>>
>>>>>>>>>> To my understanding if you want to write the total energy to a
>>>>>>>>>> file for instance for an MD simulation you need to add a section similar to:
>>>>>>>>>>
>>>>>>>>>> &MOTION
>>>>>>>>>> &MD
>>>>>>>>>> &PRINT
>>>>>>>>>> &ENERGY
>>>>>>>>>> FILENAME =cp2k.out.energy
>>>>>>>>>> &EACH
>>>>>>>>>> MD 10
>>>>>>>>>> &END EACH
>>>>>>>>>> &END ENERGY
>>>>>>>>>> &END PRINT
>>>>>>>>>> &END MD
>>>>>>>>>> &END MOTION
>>>>>>>>>>
>>>>>>>>>> In this example the energy of every tenth step is written to the
>>>>>>>>>> file, and is independent of the type of force evaluation (MM, QM, QM/MM,
>>>>>>>>>> ...).
>>>>>>>>>>
>>>>>>>>>> Here is the corresponding section in the manual:
>>>>>>>>>> https://manual.cp2k.org/trunk/CP2K_INPUT/MOTION/MD/PRINT/ENERGY/EACH.html
>>>>>>>>>>
>>>>>>>>>> Hope this helps,
>>>>>>>>>> Jadzia
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On Wednesday, September 6, 2017 at 8:31:10 AM UTC+2,
>>>>>>>>>> jts2... at gmail.com wrote:
>>>>>>>>>>>
>>>>>>>>>>> Dear researchers and developers,
>>>>>>>>>>>
>>>>>>>>>>> I am not so familiar with CP2K. After I run a QMMM simulation of
>>>>>>>>>>> KCl just as here:
>>>>>>>>>>> https://www.cp2k.org/exercises:2017_ethz_mmm:qmmm, I want to
>>>>>>>>>>> know the energy of the whole system not just the energy of the QM region,
>>>>>>>>>>> how to achieve it in the input setting?
>>>>>>>>>>>
>>>>>>>>>>> I'll appreciate for your apply !
>>>>>>>>>>>
>>>>>>>>>>
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