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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