Questions about AdBF-QM/MM in cp2k
Ivan Gladich
igla... at gmail.com
Thu Feb 2 05:59:23 UTC 2017
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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