[CP2K-user] getting error while minimising HCOOH + TMA on water surface.
Naresh Bala
nrsh... at gmail.com
Sat Nov 7 07:19:56 UTC 2020
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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