Some questions about the "UREA Zwitterion" tutorial
ywta... at gmail.com
Wed Mar 22 03:21:57 CET 2017
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
I really appreciate that many professors and developers contributed to
these helpful tutorials.
If anyone can answer these questions, it would be fantastic.
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