[CP2K-user] getting error while minimising HCOOH + TMA on water surface.

[Marcella Iannuzzi]

Try and set CONN_FILE_FORMAT OFF

Marcella


On Saturday, November 7, 2020 at 8:19:57 AM UTC+1 Naresh Bala wrote:

> Hi all,
> I want to simulate HCOOH + TMA on the water molecule. So firstly I want to 
> minimize my system using the* following cp2k input-*
>
> &GLOBAL
>   RUN_TYPE  GEO_OPT
>   PROJECT_NAME  trial3
>   PRINT_LEVEL  MEDIUM
> &END GLOBAL
> &FORCE_EVAL
>   METHOD  QUICKSTEP
>   &DFT
>     BASIS_SET_FILE_NAME  BASIS_SET.dat
>     POTENTIAL_FILE_NAME  GTH_POTENTIALS.dat
>     &XC
>       &XC_FUNCTIONAL  BLYP
>       &END XC_FUNCTIONAL
>       &VDW_POTENTIAL
>         DISPERSION_FUNCTIONAL  PAIR_POTENTIAL
>         &PAIR_POTENTIAL
>           REFERENCE_FUNCTIONAL  BLYP
>           TYPE  DFTD3(BJ)
>           PARAMETER_FILE_NAME  dftd3.dat
>           LONG_RANGE_CORRECTION  .FALSE.
>           VERBOSE_OUTPUT  TRUE
>         &END PAIR_POTENTIAL
>       &END VDW_POTENTIAL
>     &END XC
>     CHARGE  0
>     MULTIPLICITY  1
>     &QS
>       METHOD  GPW
>     &END QS
>     &SCF
>       SCF_GUESS  ATOMIC
>       MAX_SCF  150
>       EPS_SCF  1.0E-6
>       &DIAGONALIZATION
>         ALGORITHM  STANDARD
>       &END DIAGONALIZATION
>       &PRINT
>         &RESTART  ON
>           &EACH
>             GEO_OPT  100 
>           &END EACH
>         &END RESTART
>       &END PRINT
>     &END SCF
>     &MGRID
>       NGRIDS  4
>       CUTOFF  280
>       REL_CUTOFF  40
>     &END MGRID
>   &END DFT
>   &SUBSYS
>     &TOPOLOGY
>       COORD_FILE_FORMAT  PDB
>       COORD_FILE_NAME  s_input.pdb
>       &CENTER_COORDINATES
>       &END CENTER_COORDINATES
>     &END TOPOLOGY
>     &CELL
>       ABC  35 35 35
>     &END CELL
>     &KIND H2
>       ELEMENT H
>       BASIS_SET  DZV-ALL
>       POTENTIAL  GTH-BLYP
>     &END KIND
>     &KIND O
>       BASIS_SET  DZV-ALL
>       POTENTIAL  GTH-BLYP
>     &END KIND
>     &KIND H1
>       ELEMENT H
>       BASIS_SET  DZV-ALL
>       POTENTIAL  GTH-BLYP
>     &END KIND
>     &KIND C
>       BASIS_SET  DZV-ALL
>       POTENTIAL  GTH-BLYP
>     &END KIND
>     &KIND H
>       BASIS_SET  DZV-ALL
>       POTENTIAL  GTH-BLYP
>     &END KIND
>     &KIND N
>       BASIS_SET  DZV-ALL
>       POTENTIAL  GTH-BLYP
>     &END KIND
>   &END SUBSYS
> &END FORCE_EVAL
> &MOTION
>   &GEO_OPT
>     TYPE  MINIMIZATION
>     OPTIMIZER  CG
>     MAX_DR  3.00E-03
>     MAX_ITER  150
>   &END GEO_OPT
>   &PRINT
>     &RESTART  ON
>       &EACH
>         GEO_OPT  100 
>       &END EACH
>     &END RESTART
>   &END PRINT
> &END MOTION
>
>
> *But, I am getting the following error-*
> GENERATE|  Preliminary Number of Bonds generated:                          
>  593
>
>  GENERATE| WARNING in connectivity generation!
>  GENERATE| Two molecules/residues named (MOL1) have different  number of 
> atoms.
>  GENERATE| Molecule starting at position (10) has Nr. <5> of atoms.
>  GENERATE| while the other same molecules have Nr. <524> 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 (2016.251678 )
>
>
>
> *Please help, I am a novice in cp2k calculation. *
>
>
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