Grottus mechanism

[huan... at mail.huji.ac.il]

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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