[CP2K:9117] Re: Some questions about the "UREA Zwitterion" tutorial

[William Tao]

It seems that such modification will not change a lot in the results.
You can have a try.

2017-06-18 1:33 GMT-05:00 <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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