Grottus mechanism

[Dj MG]

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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