output files ALANINE.out is huge

huan... at mail.huji.ac.il huan... at mail.huji.ac.il
Wed Aug 3 09:21:14 CEST 2016


Hi,

Just to add Samuel's reply.

To reduce the volume of the output file, you need to set the keyword 
PRINT_LEVEL to LOW in the &GLOBAL section.

&GLOBAL
  ...
  PRINT_LEVEL LOW
  ...
&END GLOBAL

As mentioned by Samuel, you can extract the trajectory into the *.xyz file 
by setting the &PRINT keyword in the &MOTION section. The name of the 
trajectory file is the same as the PROJECT name in the &GLOBAL section you 
given, but with the extension of *-pos-1.xyz.

&MOTION
  ...
  &PRINT
    ...
    &TRAJECTORY
       LOG_PRINT_KEY TRUE
       FORMAT XYZ
       UNIT angstrom
       &EACH
         MD 1  # It depends on your system. Maybe you can set it as 10, 
which means to save the coordinates every 10 steps.
       &END EACH
        ADD_LAST NUMERIC
    &END TRAJECTORY
    ...
    &END PRINT
&END MOTION

I never run QM/MM, so I could not give any suggestion on your second 
question.

Regards,
Huan
.


On Saturday, July 30, 2016 at 6:58:50 PM UTC+3, tuf... at temple.edu wrote:
>
> 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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