Grottus mechanism

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

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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