Warning in connectivity generation

Alex nedo... at gmail.com
Thu Nov 23 03:02:52 CET 2017


Hi all,

I have a system that contains a molybdenum disulfide (MoS2) sample and a 
charged (+1) potassium ion. The MoS2 structure itself gets energy-minimized 
without any issues, but in combination with this ion I get a nonstop stream 
of GENERATE warnings like this: 


 GENERATE|  Preliminary Number of Bonds generated:                          
 360

 GENERATE| WARNING in connectivity generation!
 GENERATE| Two molecules/residues named (MOL1) have different  number of 
atoms.
 GENERATE| Molecule starting at position (13) has Nr. <0> of atoms.
 GENERATE| while the other same molecules have Nr. <162> of atoms!
 GENERATE| Increasing bondparm_factor by 1.05.. An error was found in the 
generated
 GENERATE| connectivity. Retry...
 GENERATE| Present value of BONDPARM_FACTOR (   Infinity ).

When I replace the potassium ion with e.g. a proton, everything is back to 
normal.

Here's the DFT section of my input:

  &DFT
    CHARGE 1
    BASIS_SET_FILE_NAME BASIS_SET2
    POTENTIAL_FILE_NAME GTH_POTENTIALS2
    &MGRID
      NGRIDS 5
      CUTOFF 500
    &END MGRID
    &QS
      METHOD GPW
    &END QS
    &SCF
      SCF_GUESS RESTART
      EPS_SCF 5.0E-6
      MAX_SCF 150
      ADDED_MOS  100
      &MIXING
          METHOD BROYDEN_MIXING
          ALPHA    0.1
          NBROYDEN   8
      &END MIXING
    &END SCF
     &XC
        &XC_FUNCTIONAL  PBE
        &END XC_FUNCTIONAL
        &VDW_POTENTIAL
          POTENTIAL_TYPE  PAIR_POTENTIAL
          &PAIR_POTENTIAL
            TYPE  DFTD3
            PARAMETER_FILE_NAME dftd3.dat
           REFERENCE_FUNCTIONAL PBE
           CALCULATE_C9_TERM  T
          &END PAIR_POTENTIAL
        &END VDW_POTENTIAL
      &END XC
  &END DFT

Any suggestions? If you need further info, please let me know. 

Thank you,

Alex
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