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 !
>>>>>>>>>>>
>>>>>>>>>>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20170911/fa6b800f/attachment.htm>


More information about the CP2K-user mailing list