Grottus mechanism

[Dj MG]

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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