[CP2K-user] [CP2K:17514] Questions about QMMM input

[Jessie wang]

Dear developers,

I'm a rookie to cp2k and computational chemistry. I have some questions 
about QMMM input and the manul of cp2k are not clear for me. I'd really 
appreciate it if you have any advise or comments on my long list of 
quesitons, LOL~ 

I'm about to running a QMMM calculation for a cluster+H2O system. The H2O 
are explicit solvent molecules in the systems and I'd like to deal with 
them by MM except for five of them which I'd like to deal by adaptive model 
(adaptive buffer).  I have several quesitons refers to the input of the 
systems.

1. In the section FORCE_EVAL/MM/FORCEFIELD,  what kind of forcefield parm 
file should I provide. The file for only MM atoms(H2O), or the whole 
systems(in my case, cluster+H2O).

2. I found some examples in /tests/, for example the 
tests/QMMM/QS/regtest-3/sio2-qmm-gauss-1.inp, did not applied any 
parm.files. Does the section &NONBONDED and &BONDED working as the same 
with parm.files?  And so for the system contains hunderds of molecule, 
which is a more complex situation of bonded and nonbonded parameters, we 
provide a parm .files for cp2k to read, am I understand it in the right way?

3. For the section of QMMM/QM_KIND,  we need to identify the MM_INDEX for 
the molecules we want to deal with QM. Does it means the working flow of 
cp2k is that define the whole system as MM first, and then pick the 
molecules out of MM and deal with QM.  

4. For the ADAPTIVE defination part.  Does the following three different 
ways actually working as the same funtion? So that I only need to use one 
of them, am I right ? And 2) seems like it can provide a more dynamic 
region of buffer and core. Does this means when I am running MD, the 
molecules enter the radii of R_QM will be deal with QM, enter the radii of 
R_BUF will be deal as buffer ect. Otherwise, the molecule moved out of the 
radii will be treat as MM? 
  1) ADAPTIVE_EXCLUDE_MOLECULES 
<https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/QMMM/FORCE_MIXING.html#list_ADAPTIVE_EXCLUDE_MOLECULES>
  2) R_BUF 
<https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/QMMM/FORCE_MIXING.html#list_R_BUF>
, R_CORE 
<https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/QMMM/FORCE_MIXING.html#list_R_CORE>
 and R_QM 
<https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/QMMM/FORCE_MIXING.html#list_R_QM>
 
  3) QM_NON_ADAPTIVE 
<https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/QMMM/FORCE_MIXING/QM_NON_ADAPTIVE.html>
 and BUFFER_NON_ADAPTIVE 
<https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/QMMM/FORCE_MIXING/BUFFER_NON_ADAPTIVE.html>

5. What does it means exactly of "buffer". I read the 
https://arxiv.org/pdf/1409.5218.pdf . And my understanding of "buffer" is a 
region of QM, which is deal with mixing forces method. I'm not sure  I am 
on the right track. 


Thank you very much


Best,
Jessie 

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