[CP2K-user] [CP2K:22003] Re: Help Required For Simulating Simple H20 Molecule Using Quickstep.
Frederick Stein
f.stein at hzdr.de
Thu Dec 18 17:36:12 UTC 2025
Dear Satchith,
I guess the culprit is the COORD-section. Remove it and use
&TOPOLOGY
COORD_FILE_NAME water.xyz
&END
instead. The parser expects the coordinates directly without the header of
the XYZ-file here.
Otherwise, please always include the actual output file or error message.
Best,
Frederick
Satchith PS schrieb am Donnerstag, 18. Dezember 2025 um 14:32:40 UTC+1:
> Hey all!
>
> I'm a student starting to learn CP2K software. I don't have much
> background in molecular dynamics simulation, have just started. From what I
> understood so far, I created an input file "water_AIMD.inp" and a separate
> coordinate file "water.xyz" as follows. They run but end abruptly. Can
> anyone please find any mistakes in these files and help me?
>
>
> *Input file:*
> @SET PROJECT water_AIMD
> @SET STEPS 20000
> @SET TIMESTEP 0.5
> @SET TEMP 300
>
> &GLOBAL
> PROJECT ${PROJECT}
> RUN_TYPE MD
> PRINT_LEVEL LOW
> &END GLOBAL
>
>
> &FORCE_EVAL
> METHOD QS
>
> &DFT
> BASIS_SET_FILE_NAME/BASIS_MOLOPT
> POTENTIAL_FILE_NAME/GTH_POTENTIALS
>
> &MGRID
> CUTOFF 400
> REL_CUTOFF 50
> &END MGRID
>
> &SCF
> SCF_GUESS ATOMIC
> EPS_SCF 1.0E-6
> MAX_SCF 50
> &OT
> MINIMIZER DIIS
> PRECONDITIONER FULL_SINGLE_INVERSE
> &END OT
> &END SCF
>
> &XC
> &XC_FUNCTIONAL PBE
> &END XC_FUNCTIONAL
> &END XC
> &END DFT
>
>
> &SUBSYS
> &CELL
> ABC 9.86 9.86 9.86
> PERIODIC XYZ
> &END CELL
>
> &COORD
> @INCLUDE water.xyz
> &END COORD
>
> &KIND O
> BASIS_SET DZVP-MOLOPT-SR-GTH
> POTENTIAL GTH-PBE
> &END KIND
>
> &KIND H
> BASIS_SET DZVP-MOLOPT-SR-GTH
> POTENTIAL GTH-PBE
> &END KIND
> &END SUBSYS
> &END FORCE_EVAL
>
>
> &MOTION
> &MD
> ENSEMBLE NVT
> STEPS ${STEPS}
> TIMESTEP ${TIMESTEP}
> TEMPERATURE ${TEMP}
>
> &THERMOSTAT
> TYPE NOSE
> &NOSE
> LENGTH 3
> TIMECON 1000
> &END NOSE
> &END THERMOSTAT
> &END MD
>
> &PRINT
> &TRAJECTORY
> FORMAT XYZ
> &EACH
> MD 10
> &END EACH
> &END TRAJECTORY
>
> &VELOCITIES
> &EACH
> MD 10
> &END EACH
> &END VELOCITIES
>
> &RESTART
> FILENAME ${PROJECT}
> ADD_LAST NUMERIC
> &EACH
> MD 200
> &END EACH
> &END RESTART
> &END PRINT
> &END MOTION
>
>
> *Coordinate file :*
> 96
> 32 water molecules, cubic box ~9.86 A
>
> O 1.000000 1.000000 1.000000
> H 1.957200 1.000000 1.000000
> H 0.760000 1.926627 1.000000
>
> O 3.000000 1.000000 1.000000
> H 3.957200 1.000000 1.000000
> H 2.760000 1.926627 1.000000
>
> O 5.000000 1.000000 1.000000
> H 5.957200 1.000000 1.000000
> H 4.760000 1.926627 1.000000
>
> O 7.000000 1.000000 1.000000
> H 7.957200 1.000000 1.000000
> H 6.760000 1.926627 1.000000
>
> O 1.000000 3.000000 1.000000
> H 1.957200 3.000000 1.000000
> H 0.760000 3.926627 1.000000
>
> O 3.000000 3.000000 1.000000
> H 3.957200 3.000000 1.000000
> H 2.760000 3.926627 1.000000
>
> O 5.000000 3.000000 1.000000
> H 5.957200 3.000000 1.000000
> H 4.760000 3.926627 1.000000
>
> O 7.000000 3.000000 1.000000
> H 7.957200 3.000000 1.000000
> H 6.760000 3.926627 1.000000
>
> O 1.000000 5.000000 1.000000
> H 1.957200 5.000000 1.000000
> H 0.760000 5.926627 1.000000
>
> O 3.000000 5.000000 1.000000
> H 3.957200 5.000000 1.000000
> H 2.760000 5.926627 1.000000
>
> O 5.000000 5.000000 1.000000
> H 5.957200 5.000000 1.000000
> H 4.760000 5.926627 1.000000
>
> O 7.000000 5.000000 1.000000
> H 7.957200 5.000000 1.000000
> H 6.760000 5.926627 1.000000
>
> O 1.000000 7.000000 1.000000
> H 1.957200 7.000000 1.000000
> H 0.760000 7.926627 1.000000
>
> O 3.000000 7.000000 1.000000
> H 3.957200 7.000000 1.000000
> H 2.760000 7.926627 1.000000
>
> O 5.000000 7.000000 1.000000
> H 5.957200 7.000000 1.000000
> H 4.760000 7.926627 1.000000
>
> O 7.000000 7.000000 1.000000
> H 7.957200 7.000000 1.000000
> H 6.760000 7.926627 1.000000
>
>
> O 1.000000 1.000000 5.000000
> H 1.957200 1.000000 5.000000
> H 0.760000 1.926627 5.000000
>
> O 3.000000 1.000000 5.000000
> H 3.957200 1.000000 5.000000
> H 2.760000 1.926627 5.000000
>
> O 5.000000 1.000000 5.000000
> H 5.957200 1.000000 5.000000
> H 4.760000 1.926627 5.000000
>
> O 7.000000 1.000000 5.000000
> H 7.957200 1.000000 5.000000
> H 6.760000 1.926627 5.000000
>
> O 1.000000 3.000000 5.000000
> H 1.957200 3.000000 5.000000
> H 0.760000 3.926627 5.000000
>
> O 3.000000 3.000000 5.000000
> H 3.957200 3.000000 5.000000
> H 2.760000 3.926627 5.000000
>
> O 5.000000 3.000000 5.000000
> H 5.957200 3.000000 5.000000
> H 4.760000 3.926627 5.000000
>
> O 7.000000 3.000000 5.000000
> H 7.957200 3.000000 5.000000
> H 6.760000 3.926627 5.000000
>
> O 1.000000 5.000000 5.000000
> H 1.957200 5.000000 5.000000
> H 0.760000 5.926627 5.000000
>
> O 3.000000 5.000000 5.000000
> H 3.957200 5.000000 5.000000
> H 2.760000 5.926627 5.000000
>
> O 5.000000 5.000000 5.000000
> H 5.957200 5.000000 5.000000
> H 4.760000 5.926627 5.000000
>
> O 7.000000 5.000000 5.000000
> H 7.957200 5.000000 5.000000
> H 6.760000 5.926627 5.000000
>
> O 1.000000 7.000000 5.000000
> H 1.957200 7.000000 5.000000
> H 0.760000 7.926627 5.000000
>
> O 3.000000 7.000000 5.000000
> H 3.957200 7.000000 5.000000
> H 2.760000 7.926627 5.000000
>
> O 5.000000 7.000000 5.000000
> H 5.957200 7.000000 5.000000
> H 4.760000 7.926627 5.000000
>
> O 7.000000 7.000000 5.000000
> H 7.957200 7.000000 5.000000
> H 6.760000 7.926627 5.000000
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