[CP2K-user] Understanding connectivity file generated in QM/MM MD simulation

[Unmesh Mondal]

Dear all,

I plan to run QM/MM simulation for Pt-H2O system. In order to have 
information for the force field parameters for H2O molecule a separate 
connectivity (in psf format: "start.psf") is provided with the coordinates. 
However, cp2k code generates its own connectivity at the beginning 
("TEST-56Pt4ang-highk-dump-1.psf"). The only difference between the two 
files is the third column under the "!NATOM" section, which I understand 
gives the information for "residue ID". 

I want to understand, how cp2k calculates the "residue ID" and why is it 
different from the input? And will the above mentioned difference in the 
connectivity files affect the simulation in the long run (although !NBOND  
and !NTHETA sections stay the same)? 

Please do correct me if any information provided seems wrong.



"start.psf"
        60 !NATOM
         1 H2O      1        H2O      O       O      -0.847600        
15.999           0
         2 H2O      1        H2O      H       H       0.423800         
1.008           0
         3 H2O      1        H2O      H       H       0.423800         
1.008           0
         4 H2O      2        H2O      O       O      -0.847600        
15.999           0
         5 H2O      2        H2O      H       H       0.423800         
1.008           0
         6 H2O      2        H2O      H       H       0.423800         
1.008           0
         7 H2O      3        H2O      O       O      -0.847600        
15.999           0
         8 H2O      3        H2O      H       H       0.423800         
1.008           0
         9 H2O      3        H2O      H       H       0.423800         
1.008           0
....

"TEST-56Pt4ang-highk-dump-1.psf"
        60 !NATOM
         1 H2O      1        H2O      O       O      -0.847600        
15.999           0
         2 H2O      1        H2O      H       H       0.423800         
1.008           0
         3 H2O      1        H2O      H       H       0.423800         
1.008           0
         4 H2O      1        H2O      O       O      -0.847600        
15.999           0
         5 H2O      1        H2O      H       H       0.423800         
1.008           0
         6 H2O      1        H2O      H       H       0.423800         
1.008           0
         7 H2O      1        H2O      O       O      -0.847600        
15.999           0
         8 H2O      1        H2O      H       H       0.423800         
1.008           0
         9 H2O      1        H2O      H       H       0.423800         
1.008           0
....

Attached is the directory (send_qmmm) of a working example of the system. 
The two connectivity files discussed are inside the directory. 

Regards,
Unmesh Mondal
I-PhD student, IISER Pune, India
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