Simulating liquid DMSO
Henrique Junior
Hi everyone, I hope you are all doing fine.
CP2K is completely new for me, and it is proving to be a challenge. I am attempting to simulate liquid DMSO (a simple molecule with 10 atoms) just as a test. So far, I have tried to build my input based on tutorials simulating liquid water and tweaking it for DMSO.
The calculation is running fine and converging quite smoothly but looking at the DMSO-pos-1.xyz file that’s being generated I can see that the atoms are barely shaking. I’m attaching (and showing below) my input and the xyz file. Any help would be much appreciated.
Thanks in advance.
Vvvvvvvvvvvvvvvvvvvvvvvvvv INPUT vvvvvvvvvvvvvvvvvvvvvvvvvv
&GLOBAL
PROJECT DMSO
RUN_TYPE MD
&END GLOBAL
&FORCE_EVAL
METHOD Quickstep
&DFT
BASIS_SET_FILE_NAME GTH_BASIS_SETS
POTENTIAL_FILE_NAME GTH_POTENTIALS
CHARGE 0
MULTIPLICITY 1
&MGRID
CUTOFF [Ry] 400
&END
&QS
METHOD GPW
EPS_DEFAULT 1.0E-10
EXTRAPOLATION ASPC
&END
&POISSON
PERIODIC XYZ ! the default, gas phase systems should have 'NONE' and a wavelet solver
&END
&PRINT
&E_DENSITY_CUBE OFF
&END E_DENSITY_CUBE
&MO_CUBES
NLUMO 4
NHOMO 4
WRITE_CUBE .FALSE.
&EACH
MD 10
&END
&END
&END
&SCF
SCF_GUESS ATOMIC
MAX_SCF 500
EPS_SCF 1.0E-6
&OT
PRECONDITIONER FULL_SINGLE_INVERSE
MINIMIZER DIIS
&END OT
&OUTER_SCF ! repeat the inner SCF cycle 10 times
MAX_SCF 10
EPS_SCF 1.0E-6
&END
&PRINT
&RESTART OFF
&END
&END
&END SCF
&XC
&XC_FUNCTIONAL
&PBE
&END
&END XC_FUNCTIONAL
! adding Grimme's D3 correction (by default without C9 terms)
&VDW_POTENTIAL
POTENTIAL_TYPE PAIR_POTENTIAL
&PAIR_POTENTIAL
PARAMETER_FILE_NAME dftd3.dat
TYPE DFTD3
REFERENCE_FUNCTIONAL PBE
R_CUTOFF [angstrom] 16
&END
&END VDW_POTENTIAL
&END XC
&END DFT
&SUBSYS
&CELL
ABC [angstrom] 9.0 9.0 9.0
&END CELL
&TOPOLOGY
COORD_FILE_NAME DMSOcaixa.xyz
COORD_FILE_FORMAT XYZ
&END
&KIND H
BASIS_SET DZVP-MOLOPT-SR-GTH
POTENTIAL GTH-PBE-q1
&END KIND
&KIND C
BASIS_SET DZVP-MOLOPT-SR-GTH
POTENTIAL GTH-PBE-q4
&END KIND
&KIND O
BASIS_SET DZVP-MOLOPT-SR-GTH
POTENTIAL GTH-PBE-q6
&END KIND
&KIND S
BASIS_SET DZVP-MOLOPT-SR-GTH
POTENTIAL GTH-PBE-q6
&END KIND
&END SUBSYS
&END FORCE_EVAL
! how to propagate the system, selection via RUN_TYPE in the &GLOBAL section
&MOTION
&PRINT
&TRAJECTORY
&EACH
MD 1
&END EACH
&END TRAJECTORY
&VELOCITIES OFF
&END VELOCITIES
&FORCES OFF
&END FORCES
&RESTART_HISTORY
&EACH
MD 500
&END EACH
&END RESTART_HISTORY
&RESTART
BACKUP_COPIES 3
&EACH
MD 1
&END EACH
&END RESTART
&END PRINT
&GEO_OPT
OPTIMIZER BFGS ! Good choice for 'small' systems (use LBFGS for large systems)
MAX_ITER 100
MAX_DR [bohr] 0.003 ! adjust target as needed
&BFGS
&END
&END
&MD
ENSEMBLE NVT ! sampling the canonical ensemble, accurate properties might need NVE
TEMPERATURE [K] 300
TIMESTEP [fs] 0.5
STEPS 1000
# GLE thermostat as generated at http://epfl-cosmo.github.io/gle4md
# GLE provides an effective NVT sampling.
&THERMOSTAT
REGION MASSIVE
TYPE GLE
&GLE
NDIM 5
A_SCALE [ps^-1] 1.00
A_LIST 1.859575861256e+2 2.726385349840e-1 1.152610045461e+1 -3.641457826260e+1 2.317337581602e+2
A_LIST -2.780952471206e-1 8.595159180871e-5 7.218904801765e-1 -1.984453934386e-1 4.240925758342e-1
A_LIST -1.482580813121e+1 -7.218904801765e-1 1.359090212128e+0 5.149889628035e+0 -9.994926845099e+0
A_LIST -1.037218912688e+1 1.984453934386e-1 -5.149889628035e+0 2.666191089117e+1 1.150771549531e+1
A_LIST 2.180134636042e+2 -4.240925758342e-1 9.994926845099e+0 -1.150771549531e+1 3.095839456559e+2
&END GLE
&END THERMOSTAT
&END
&END
Thomas Kühne
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<DMSO.inp><DMSO-pos-1.xyz>
DMITRII Drugov
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