massive QMMM output file and system setup
tuf6... at temple.edu
tuf6... at temple.edu
Sun Jul 31 13:22:19 UTC 2016
Hello CP2K users,
I am running QMMM simulation of 1 di alanine in 5000 methanol molecules. My
system deals with alanine and 25 methanol molecule in QM region and rest in
MM region using the attached input file.
I want to know why my alanine.out file is huge as for only 1000 steps it is
~3 GB.
My main question is that is this input file is good enough to start qmmm or
i need some additional parameters....
I hv doubt about some key point mentioned in input file in
* bold redThank you *
&FORCE_EVAL
METHOD QMMM
#------------------------------------------------------------------------------
&DFT
BASIS_SET_FILE_NAME ./GTH_BASIS_SETS
POTENTIAL_FILE_NAME ./GTH_POTENTIALS
&MGRID
COMMENSURATE
CUTOFF 300
&END MGRID
&QS
&END QS
&SCF
# SCF_GUESS atomic
MAX_SCF 30
EPS_SCF 1.0E-6
SCF_GUESS ATOMIC
&OUTER_SCF
EPS_SCF 1.0E-6
MAX_SCF 10
&END OUTER_SCF
&OT
PRECONDITIONER FULL_SINGLE_INVERSE
MINIMIZER DIIS
&END OT
&PRINT
&RESTART
&EACH
MD 10
&END EACH
FILENAME =ABC.RESTART
&END RESTART
&RESTART_HISTORY OFF
&END RESTART_HISTORY
&END PRINT
&END SCF
&XC
&XC_GRID
XC_SMOOTH_RHO NN10
XC_DERIV NN10_SMOOTH
&END XC_GRID
&XC_FUNCTIONAL BLYP
&END XC_FUNCTIONAL
&vdW_POTENTIAL
POTENTIAL_TYPE PAIR_POTENTIAL
&PAIR_POTENTIAL
TYPE DFTD3
PARAMETER_FILE_NAME ./dftd3.dat
REFERENCE_FUNCTIONAL BLYP
CALCULATE_C9_TERM .TRUE.
REFERENCE_C9_TERM .TRUE.
&END PAIR_POTENTIAL
&END vdW_POTENTIAL
&END XC
&END DFT
#------------------------------------------------------------------------------
&MM
&FORCEFIELD
PARM_FILE_NAME ala_big.top
PARMTYPE AMBER
&SPLINE
EMAX_SPLINE 1.0 *# is it enough or need higher how to check *
RCUT_NB 10
&END
&END FORCEFIELD
&POISSON
&EWALD
EWALD_TYPE ewald
ALPHA .44
GMAX 21
&END EWALD
&END POISSON
&END MM
#------------------------------------------------------------------------------
&QMMM
&CELL
ABC 25.0 25.0 25.0 *# it will be periodic or not most confusing for
me .....*
&END CELL
ECOUPL GAUSS
USE_GEEP_LIB 7 *# why 7 i just got the range from cp2k manual
0-15*
&QM_KIND O
MM_INDEX 8 18 669 3081 3609 3813 4563 6375 9261 10821 11295 12795
MM_INDEX 13029 13053 13551 13695 14979 15069 17613 17853 18447 18471
MM_INDEX 18891 19809 19875 25971 26709
&END QM_KIND
&QM_KIND N
MM_INDEX 5 15
&END QM_KIND
&QM_KIND C
MM_INDEX 1 7 9 10 17 19 666 3078 3606 3810 4560 6372 9258 10818 11292
MM_INDEX 12792 13026 13050 13548 13692 14976 15066 17610 17850 18444
MM_INDEX 18468 18888 19806 19872 25968 26706
&END QM_KIND
&QM_KIND H
MM_INDEX 2 3 4 6 11 12 13 14 16 20 21 22
&END QM_KIND
&QM_KIND H
MM_INDEX 665 3077 3605 3809 4559 6371 9257 10817 11291 12791 13025
13049
MM_INDEX 13547 13691 14975 15065 17609 17849 18443 18467 18887 19805
19871 25967 26705
&END QM_KIND
&QM_KIND H
MM_INDEX 667 3079 3607 3811 4561 6373 9259 10819 11293 12793 13027
13051 13549
MM_INDEX 13693 14977 15067 17611 17851 18445 18469 18889 19807 19873
25969 26707
&END QM_KIND
&QM_KIND H
MM_INDEX 668 3080 3608 3812 4562 6374 9260 10820 11294 12794 13028
13052 13550
MM_INDEX 13694 14978 15068 17612 17852 18446 18470 18890 19808 19874
25970 26708
&END QM_KIND
&QM_KIND H
MM_INDEX 670 3082 3610 3814 4564 6376 9262 10822 11296 12796 13030
13054 13552 13696
MM_INDEX 14980 15070 17614 17854 18448 18472 18892 19810 19876 25972
26710
&END QM_KIND
&END QMMM
#------------------------------------------------------------------------------
&SUBSYS
&CELL
ABC 67.283 67.283 67.283 *# it should be periodic or not
.....*
&END CELL
&TOPOLOGY
COORDINATE CRD
COORD_FILE_NAME ./ala_big.crd
CONNECTIVITY AMBER
CONN_FILE_NAME ./ala_big.top
&END
&KIND H
BASIS_SET TZV2P-GTH
POTENTIAL GTH-BLYP-q1
MASS 2.0
&END KIND
&KIND O
BASIS_SET TZV2P-GTH
POTENTIAL GTH-BLYP-q6
&END KIND
&KIND C
BASIS_SET TZV2P-GTH
POTENTIAL GTH-BLYP-q4
&END KIND
&KIND N
BASIS_SET TZV2P-GTH
POTENTIAL GTH-BLYP-q5
&END KIND
&END SUBSYS
&END FORCE_EVAL
#------------------------------------------------------------------------------
&GLOBAL
PROJECT ALANINE
RUN_TYPE MD
&END GLOBAL
&MOTION
&MD
ENSEMBLE NVT
STEPS 1000
TIMESTEP 1.0
TEMPERATURE 300
&THERMOSTAT
TYPE CSVR
&CSVR
TIMECON 20
&END CSVR
&END THERMOSTAT
&PRINT
&ENERGY
&EACH
MD 2
&END EACH
FILENAME =ABC.ene
&END ENERGY
&END PRINT
&END MD
&END MOTION
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