Grottus mechanism

[Dj MG]

OK thank you very much Huan. God bless you.

On Saturday, July 16, 2016 at 12:19:19 AM UTC+7, hua... at mail.huji.ac.il 
wrote:
>
> Sorry, I do not have any experience on QM/MM
>
> On Friday, July 15, 2016 at 2:42:07 PM UTC+3, Dj MG wrote:
>>
>> Huan, Could you help me find the error part of my qmmm input files?
>>
>> On Friday, July 15, 2016 at 3:15:36 PM UTC+7, hua... at mail.huji.ac.il 
>> wrote:
>>>
>>> Dear Dj MG,
>>>
>>> As I mentioned in the last reply, the Martyna-Tuckerman (MT) 
>>> Poisson_solver was proposed for isolated molecules (or clusters). 
>>>
>>> That is the same condition as you want to simulate, the protonated water 
>>> dimer (H3O^+ H2O), which is NOT the periodic system.
>>>
>>> I suggest to read the reference *ChemPhysChem*, 2011, 12, 1906 - 1915, 
>>> in which most of the parameters were listed in the Methods section.
>>>
>>> All the best,
>>> Huan
>>> .
>>>
>>>
>>> On Thursday, July 14, 2016 at 6:25:13 PM UTC+3, Dj MG wrote:
>>>>
>>>> OK Huan, i'll try it. Could i know what is the reason you suggestion me 
>>>> to add MT?
>>>>
>>>> On Thursday, July 14, 2016 at 9:52:45 PM UTC+7, hua... at mail.huji.ac.il 
>>>> wrote:
>>>>>
>>>>> Dear DJ MG,
>>>>>
>>>>> The CPK representation only shows the "fixed bond". It is good for the 
>>>>> snapshot published in journals, since it is only a picture. However, when 
>>>>> displaying your simulation with proton transfer event, the OH bond will 
>>>>> break in H3O^+ part and will form a new OH bond in the H2O part. It is a 
>>>>> dynamic process. As a result, the "dynamicbond" is more suitable than CPK 
>>>>> representation.
>>>>>
>>>>> Let's go back to your input file.
>>>>>
>>>>> As you said, the system you want to simulate is a dimer cluster. So, 
>>>>> in the &POISSON section, you need to specify the parameter of 
>>>>> PERIODIC as NONE, not XYZ. 
>>>>> In addition, you need to use the Martyna-Tuckerman POSSION_SOLVER, as 
>>>>> shown in  
>>>>> https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/DFT/POISSON/MT.html
>>>>> This Poisson solver was proposed for the isolated molecules or 
>>>>> clusters in the simulation box.
>>>>>
>>>>> Keeping the default values for the parameters of ALPHA and REL_CUTOFF 
>>>>> would be fine.
>>>>>
>>>>> &POISSON
>>>>>   PERIODIC NONE
>>>>>   POISSON_SOLVER  MT
>>>>>   &MT
>>>>>      ALPHA 7.0
>>>>>      REL_CUTOFF 2.0
>>>>>   &END MT
>>>>> &END POISSON
>>>>>
>>>>>
>>>>> In the QS section,  it is better to set EXTRAPOLATION_ORDER as 3. 
>>>>>
>>>>> In the &SUBSYS  &CELL section, you also need to specify the PERIODIC 
>>>>> as NONE, which was not shown in your input file.
>>>>> You can try to increase the dimension of your simulation box, perhaps 
>>>>> increase to 15.0 angstrom. 
>>>>>
>>>>>  &SUBSYS
>>>>>    &CELL
>>>>>        PERIODIC  NONE
>>>>>        ABC  15.0  15.0  15.0
>>>>>    &END CELL
>>>>> ...
>>>>>
>>>>>
>>>>> I hope those suggestions would be helpful.
>>>>>
>>>>> All the best,
>>>>> Huan
>>>>> .
>>>>>
>>>>>
>>>>>
>>>>> On Thursday, July 14, 2016 at 1:41:44 PM UTC+3, Dj MG wrote:
>>>>>>
>>>>>> OK thank you Huan. I owe you one. I'm beginner in cp2k and english is 
>>>>>> not my Mother tongue. So that only i can do is try exercises in cp2k 
>>>>>> website and try and try more. OK i will try your suggestion. And your first 
>>>>>> suggestion was succeed to change drawing method. My question is why in CPK 
>>>>>> is failed to visualize the H+ transport?. The fact a lot of journal using 
>>>>>> CPK model. 
>>>>>>
>>>>>> My system is small dimer cluster, any suggestion for this case?
>>>>>>
>>>>>> DJ MG
>>>>>> Cheers Always
>>>>>>
>>>>>> On Wednesday, July 13, 2016 at 4:52:11 PM UTC+7, 
>>>>>> hua... at mail.huji.ac.il wrote:
>>>>>>>
>>>>>>> Dear Dj MG,
>>>>>>>
>>>>>>> I checked your files. Actually, the proton has transferred from 
>>>>>>> H3O^+ to H2O in your short trajectory.
>>>>>>>
>>>>>>> You may use the program called VMD to visualize the position file, 
>>>>>>> which is your "H3O+_H2O-pos-1.xyz". 
>>>>>>>
>>>>>>> By adding the representation with the "Drawing Method" of 
>>>>>>> "dynamicbonds", and setting the "Distance Cutoff" as 1.2, you will be able 
>>>>>>> to observe the proton transfer event.
>>>>>>>
>>>>>>> The questions in your input file are:
>>>>>>>
>>>>>>> 1) Why you set the "MULTIPLICITY" as 3 in your input file? 
>>>>>>> The proton does not have electron, and all electrons in H3O^+ H2O 
>>>>>>> system are in-pair. In my opinion, the multiplicity for this system should 
>>>>>>> be 1.
>>>>>>>
>>>>>>> 2) What kind of system would you like to simulate? Periodic system 
>>>>>>> or just a small dimer cluster?
>>>>>>>
>>>>>>> 3) The temperature printed in your output file fluctuated quite 
>>>>>>> large. The target temperature you set is 313 K, however, as shown in 
>>>>>>> your "H3O+_H2O-1.ener" file, the maximum value even reached to 1339 K, 
>>>>>>> whereas the minimum value dropped down to 99 K. That seems quite 
>>>>>>> unreasonable. You need to choose a better thermostat, like Nose-Hoover 
>>>>>>> chain thermostat or CSVR thermostat.
>>>>>>>
>>>>>>> All the best,
>>>>>>> Huan
>>>>>>> .
>>>>>>>
>>>>>>>
>>>>>>> On Tuesday, July 12, 2016 at 6:19:40 PM UTC+3, Dj MG wrote:
>>>>>>>>
>>>>>>>> Hello cp2k lovers. 
>>>>>>>> I have project which aims to simulate proton transfer through 
>>>>>>>> grottus mechanism using aimd.
>>>>>>>> I got a problem, why H atoms from H3O+ can't move to H2O?
>>>>>>>> I attached my files below.
>>>>>>>>
>>>>>>>>
>>>>>>>> Cheers Always
>>>>>>>> ...
>>>>>>>>
>>>>>>>
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