Questions about AdBF-QM/MM in cp2k

[Ivan Gladich]

Dear Cp2K users,

I am a newbie of CP2K and I am trying to use Adaptive Buffered force QM-MM 
(AdBF-QM/MM) in cp2k

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4351341/

 to study a radical specie in water
I have a couple of questions.

1) Using

...

  &QMMM


    &QM_KIND Br

      MM_INDEX  1

    &END QM_KIND 

    

    &QM_KIND O1

      MM_INDEX  2

    &END QM_KIND 


    &FORCE_MIXING

MAX_N_QM 500

         R_CORE 0.0 0.1 #dimension of the core region for the reduced QM/MM 
calculation. Could be 0 if you have the force field

         R_QM   3.0 3.5  #Dimension of the dynamical core region

         R_BUF  3.0 3.5  #dimensione of the buffere region 

         QM_KIND_ELEMENT_MAPPING Br Br #atoms that can be adaptively 
selectefor the QM region

         QM_KIND_ELEMENT_MAPPING O O  #atoms that can be adaptively 
selected for the QM region

         QM_KIND_ELEMENT_MAPPING H H  #atoms that can be adaptively 
selectedfor the QM region

         EXTENDED_DELTA_CHARGE  0 # this is the charge of the QM_dynamical 
+ buffer region. 

         MOMENTUM_CONSERVATION_REGION  QM #only to dynamical core, you can 
also choose BUFFER for QM+BUFFER

         MOMENTUM_CONSERVATION_TYPE   EQUAL_A #equal acceleration on each 
atom, or EQUAL_F, equal force

   &END FORCE_MIXING
....

And I got in my output

QMMM FORCE MIXING final count (not including links):  N_QM core_list      2 
N_QM core     0 N_QM extended    12 N_QM buffered    63

QMMM FORCE MIXING final count (not including links):  N_QM core_list      2 
N_QM core     0 N_QM extended    12 N_QM buffered    63

QMMM FORCE MIXING final count (not including links):  N_QM core_list      2 
N_QM core     0 N_QM extended    12 N_QM buffered    63

QMMM FORCE MIXING final count (not including links):  N_QM core_list      2 
N_QM core     0 N_QM extended    12 N_QM buffered    63

QMMM FORCE MIXING final count (not including links):  N_QM core_list      2 
N_QM core     0 N_QM extended    12 N_QM buffered    63


...


Is N_QM core = 0 the number of atoms in my dynamical QM region? 

Moreover, reading the paper N_QM extended "is constructed adding a buffer 
region around the QM dynamical core"

But N_QM extended =12 and N_QM buffered is 63, so it cannot be (N_QM should 
be the same of the buffer plus the dynamical core)...


2) How does the R_BUF and R_QM works?


 R_BUF is a radius around each atoms belonging to the QM dynamical core 
region


OR


R_BUF is centered around the QM_CORE (in my case determined by Br and O 
position) and, thus, I should impose always R_QM =< R_BUF ?


3) Is it possible to write, at each time step of my run, a label or the 
indexes of the atoms in the dynamical and extended QM/MM region?


I tried using


      &FORCE_MIXING_LABELS

         FORMAT XYZ

         &EACH

            MD 1

         &END EACH

         COMMON_ITERATION_LEVELS 0

      &END FORCE_MIXING_LABELS


but it seems that it labels only the atoms in the QM CORE, i.e., 
*fmlabels-1_23.xyz


    6482

 i =       23, time =       11.500, E =       -21.9207476721

 BR        10.0000000000       10.0000000000       10.0000000000

  O        10.0000000000       10.0000000000       10.0000000000

  O         0.0000000000        0.0000000000        0.0000000000

  H         0.0000000000        0.0000000000        0.0000000000

  H         0.0000000000        0.0000000000        0.0000000000

...


Thank you for any possible help or comment


Best Regards

Ivan



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