Some questions about the "UREA Zwitterion" tutorial

William Tao ywta... at gmail.com
Wed Mar 22 03:21:57 CET 2017


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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