Some questions about the "UREA Zwitterion" tutorial

[William Tao]

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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