Some questions about the "UREA Zwitterion" tutorial

[jts2t... at gmail.com]

Hello William, I want to know the influence of the change from {*38.8605230 
 39.1154930  39.2709120*} to {*22.564  22.699  22.781*}. Does the output 
change a lot?

在 2017年4月6日星期四 UTC+8下午11:57:16，William Tao写道：
>
> Now I have understood much better for my own problems.
>
> 1) The cell size (ABC) for the 1st step MM Equilibrium is too large. I 
> guess the author didn't convert the {*38.8605230  39.1154930  39.2709120* } 
> which is in the unit of Bohr into Angstrom.  So, right now I changed this 
> into "*ABC  22.564  22.699  22.781*". 
>
> 2) NPT then NVT, now it is clear to me.
>
>
> Please correct me if I am wrong, especially with regard to the (1) 
> question.
>
>
> William
>
>
>
> 在 2017年3月21日星期二 UTC-5下午9:21:57，William Tao写道：
>>
>> Hello World,
>>
>> I have been learning cp2k calculation with tutorials on the website. And 
>> I have a few questions about the tutorial by Professor Iannuzzi, "QM/MM 
>> study of UREA Zwitterion in water 
>> <https://www.cp2k.org/exercises:2015_cecam_tutorial:urea#fourth_taskqm_mm_metadyanamics_simulations>
>> ".
>>
>> 1) In the first task of "First task: MM isobaric/isothermal ensemble", 
>> the cell size is specified as "ABC [angstrom] 38.8605230  39.1154930 
>>  39.2709120", I do not know where these numbers are from. I measured the 
>> initial length of the cubic box generated from ambertools, it is around 
>> only 20 angstroms.
>>
>> 2) The second question is about the procedure of calculation. We do the 
>> NPT in the first step, why do we need to do the following NVT ensemble in 
>> the second and third step?
>>
>> 3) How to correctly visualize the result of step 1(The NPT ensemble) in 
>> VMD?(I saw the whole system seems to be shifting here and there) Should we 
>> expect a rectangular unit cell for the whole system? Does CP2K have the 
>> functionality of "wrap" that can move atoms outside the unit cell back into 
>> the box? 
>>
>> I really appreciate that many professors and developers contributed to 
>> these helpful tutorials. 
>>
>> If anyone can answer these questions, it would be fantastic.
>>
>> Thanks.
>>
>> William
>>
>>
>>
>>
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