Grottus mechanism

Dj MG ghada... at
Thu Jul 14 13:46:16 UTC 2016

Dear Huan. I have changed the thermostat using nose and csvr. Both of show 
the over temperature. What else should i change in my input file?  

On Thursday, July 14, 2016 at 5:41:44 PM UTC+7, 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?
> Cheers Always
> On Wednesday, July 13, 2016 at 4:52:11 PM UTC+7, hua... at 
> 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 "". 
>> 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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