The energy of the whole system in a QMMM simulation

Jadzia c.gor... at gmail.com
Fri Sep 15 04:28:02 UTC 2017
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Multiscale simulations are one of my areas as well (others are for instance 
free energy computations... :-)

Regarding the physical properties you are interested in, RDFs are much 
easier to compute than free energies (they are an own field of research), 
so you might want to avoid the latter.

Good luck with your simulations. 



On Wednesday, September 13, 2017 at 9:33:20 AM UTC+2, jts2... at gmail.com 
wrote:
>
> 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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