# Some questions about the "UREA Zwitterion" tutorial

jts2t... at gmail.com jts2t... at gmail.com
Sun Jun 18 06:33:21 UTC 2017

```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?

>
> 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
>> ".
>>
>> 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
>>
>> If anyone can answer these questions, it would be fantastic.
>>
>> Thanks.
>>
>> William
>>
>>
>>
>>
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