The energy of the whole system in a QMMM simulation

jts2t... at gmail.com jts2t... at gmail.com
Wed Sep 13 07:33:20 UTC 2017
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What a coincidence !

Yeah, I have been reading papers concerned with QMMM to find some physical 
properties they are interested in. Free energy, RDF, etc.


By the way, what subject are you concentrated in ? I major in multiscale 
calculation. 

在 2017年9月13日星期三 UTC+8上午11:21:16，Jadzia写道：
>
> Glad I could help. By the way, I'm a mathematician specialized in 
> computational science as well... :-)
>
> I don't think one can say that QM/MM is generally superior over MM models. 
> It will depend on many factors whether QM/MM can be considered as superior, 
> e.g. on the molecular system or the properties one is interested in. There 
> are MM force fields specialized for certain systems which can outperform 
> QM/MM simulations for certain properties. So the question is what 
> properties are you interested in? If you generally want to show that QM/MM 
> can be superior for certain properties, then I one idea would be to read 
> articles about QM/MM methods since they sometimes show that the QM/MM 
> method is better for certain properties than MM. The reference value for 
> comparison is ideally an experimental value of high quality, but sometimes 
> also a pure QM computation of high quality. 
>
>
>
>
>
> On Monday, September 11, 2017 at 1:28:09 PM UTC+2, jts2... at gmail.com 
> wrote:
>>
>> 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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