[CP2K-user] QM/MM high temperature

[Tianshu Jiang]

Hi Tarak,

The same situation occurred in my run, have you got any solution?
Thanks.

在 2014年2月26日星期三 UTC+8下午1:58:56，tarak写道：
>
> Any suggestions?
>
>
> On Fri, Feb 21, 2014 at 2:00 PM, tarak karmakar <ta... at gmail.com 
> <javascript:>> wrote:
>
>> Dear All,
>>
>> I have set up a QM/MM system by taking an organic molecule in 40x40x40 
>> water box. The quantum region contains the organic molecule and 23 water 
>> molecules in a periodic box of 25x25x25 ang^3. Then I am trying to run a 
>> short NVT, the input is given below.
>>
>> &FORCE_EVAL
>>   METHOD QMMM
>> #.................................................. 
>>   &DFT
>>      CHARGE -3
>>      ROKS
>>      BASIS_SET_FILE_NAME  GTH_BASIS_SETS
>>      POTENTIAL_FILE_NAME  GTH_POTENTIALS
>>     &MGRID
>>        CUTOFF 280
>>        COMMENSURATE
>>     &END MGRID
>>     
>>     &SCF
>>                     ## Max iterations and convergence limit for 
>> minimization
>>      EPS_SCF 1.0e-7
>>      MAX_SCF 250
>>                                 ## initial wavefunction guess. If no 
>> restart file, does atomic?
>>      SCF_GUESS RESTART                 ##atomic,restart,random,or core
>>                     ## Orbital transformation method helps converge more 
>> rapidly
>>       &OT ON
>>                     ## precondition the matrix with the kinetic energy. 
>> Helps diagonalize quick
>>     PRECOND_SOLVER INVERSE_CHOLESKY
>>     PRECONDITIONER FULL_KINETIC
>>                     ## Use a conjugate gradient minimizer
>>     MINIMIZER CG
>>     ROTATION .TRUE.
>>       &END OT
>>     &END SCF
>>
>>     &QS
>>       EPS_DEFAULT 1.0E-10
>>       MAP_CONSISTENT
>>       EXTRAPOLATION ASPC
>>       EXTRAPOLATION_ORDER 3
>>     &END QS
>>     &XC
>>       &XC_GRID
>>         XC_SMOOTH_RHO NN10
>>         XC_DERIV SPLINE2_SMOOTH
>>       &END XC_GRID
>>       &XC_FUNCTIONAL BLYP
>>       &END XC_FUNCTIONAL
>>     &END XC
>>     &POISSON
>>       POISSON_SOLVER MULTIPOLE
>>       PERIODIC NONE
>>     &END POISSON
>>   &END DFT
>>  #.....................................................
>>
>>   &MM
>>     &FORCEFIELD
>>      parm_file_name ./omp_new_parm.pot
>>       parmtype CHM
>>       EI_SCALE14 1.0
>>       &SPLINE
>>         EMAX_SPLINE 1.0E8
>>         RCUT_NB 12.0
>>       &END
>>     &END FORCEFIELD
>>    
>>     &POISSON
>>       &EWALD
>>         EWALD_TYPE spme
>>         ALPHA .5
>>         GMAX 37
>>         O_SPLINE 6
>>       &END EWALD
>>     &END POISSON
>>     &PRINT
>>        &FF_INFO 
>>        &END FF_INFO
>>     &END PRINT   
>>   &END MM
>>  #..........................................................
>>
>>   &QMMM
>>     E_COUPL GAUSS
>>     USE_GEEP_LIB  7
>>     &CELL
>>       ABC [angstrom] 20.0 20.0 20.0
>>       PERIODIC XYZ
>>     &END CELL
>>     &PERIODIC
>>        GMAX 1
>>       &MULTIPOLE
>>          EWALD_PRECISION 0.000001 
>>          RCUT 30.0
>>          ANALYTICAL_GTERM
>>       &END MULTIPOLE
>>     &END PERIODIC
>>     &INTERPOLATOR
>>         EPS_R 1.0e-14
>>     EPS_X 1.0e-14
>>     MAXITER 150
>>     &END INTERPOLATOR
>>
>>     &QM_KIND C
>>       MM_INDEX 2 3 7 9 12 14 16 20 24 32 
>>     &END QM_KIND
>>     &QM_KIND H
>>       MM_INDEX 6 10 13 15 17 19 21 23 25 26 171 172 756 757 960 961 1440 
>> 1441 1929 1930 2028 2029 2097 2098 2385 2386 2403 2404 2631 2632 2802 2803 
>> 2865 2866 2877 2878 3408 3409 3528 3529 3537 3538 3633 3634 3684 3685 3783 
>> 3784 4431 4432 4719 4720 4860 4861 5331 5332  
>>     &END QM_KIND
>>     &QM_KIND N
>>       MM_INDEX 1 5
>>     &END QM_KIND
>>     &QM_KIND O
>>       MM_INDEX 4 8 11 18 22 27 29 30 31 33 34  170 755 959 1439 1928 2027 
>> 2096 2384 2402 2630 2801 2864 2876 3407 3527 3536 3632 3683 3782 4430 4718 
>> 4859 5330 
>>     &END QM_KIND
>>     &QM_KIND P
>>       MM_INDEX 28
>>     &END QM_KIND
>>   &END QMMM
>> #...........................................................
>>
>>   &SUBSYS
>>     &CELL
>>       ABC [angstrom] 39.327 39.254 39.299 
>>       PERIODIC XYZ
>>     &END CELL
>>     &KIND H
>>       BASIS_SET aug-TZV2P-GTH
>>       POTENTIAL GTH-BLYP-q1
>>     &END KIND
>>     &KIND O
>>       BASIS_SET aug-TZV2P-GTH
>>       POTENTIAL GTH-BLYP-q6
>>     &END KIND
>>     &KIND N
>>       BASIS_SET aug-TZV2P-GTH
>>       POTENTIAL GTH-BLYP-q5
>>     &END KIND
>>     &KIND C
>>       BASIS_SET aug-TZV2P-GTH
>>       POTENTIAL GTH-BLYP-q4
>>     &END KIND 
>>     &KIND P
>>       BASIS_SET aug-TZV2P-GTH
>>       POTENTIAL GTH-BLYP-q5
>>     &END KIND
>>     &TOPOLOGY
>>       COORDINATE PDB
>>       COORD_FILE_NAME ./omp_lig_af_200ps_NPT.pdb
>>       CONNECTIVITY UPSF
>>       CONN_FILE_NAME ./omp_lig_c_autopsf_solv_ions.psf
>>     &END
>>   &END SUBSYS
>> &END FORCE_EVAL
>>
>> #****************************************************************
>> &GLOBAL
>>   PROJECT omp_lig_md
>>   RUN_TYPE MD
>>   PRINT_LEVEL MEDIUM
>> &END GLOBAL
>> #**************************************************************
>>
>> &MOTION
>>   &MD
>>    ENSEMBLE NVT
>>    STEPS 40000
>>    TIMESTEP 0.5
>>    TEMPERATURE 300
>>    &THERMOSTAT
>>       &NOSE
>>         LENGTH 3
>>         YOSHIDA 3
>>         TIMECON 2000
>>         MTS 2
>>       &END NOSE
>>     &END
>>     &PRINT
>>       &ENERGY
>>         &EACH
>>           MD 100
>>         &END EACH
>>       &END ENERGY
>>     &END PRINT
>>   &END MD
>>   &PRINT
>>     &RESTART
>>       &EACH
>>         MD 100
>>       &END EACH
>>     &END RESTART
>>     &RESTART_HISTORY OFF
>>     &END RESTART_HISTORY
>>
>>     &TRAJECTORY SILENT
>>       FORMAT DCD
>>       &EACH
>>         MD 100
>>       &END EACH
>>     &END TRAJECTORY
>>     
>>     &VELOCITIES OFF
>>           LOG_PRINT_KEY T
>>           FORMAT XYZ
>>           UNIT angstrom
>>           &EACH
>>             MD 100
>>           &END EACH
>>           ADD_LAST NUMERIC
>>     &END VELOCITIES
>>     
>>     &FORCES OFF
>>     &END FORCES
>>   &END PRINT
>> &END MOTION
>> #....................END......................................
>>
>> At the first NVT step the temperature of the system is very high 
>>
>>
>> *******************************************************************************
>>  ENSEMBLE TYPE                
>> =                                              NVT
>>  STEP NUMBER                  
>> =                                                1
>>  TIME [fs]                    =                                         
>> 0.500000
>>  CONSERVED QUANTITY [hartree] =                              
>> -0.589910746226E+03
>>
>>                                               INSTANTANEOUS             
>> AVERAGES
>>  CPU TIME [s]                 =                     5909.45              
>> 5909.45
>>  ENERGY DRIFT PER ATOM [K]    =          0.499380591190E+04   
>> 0.000000000000E+00
>>  POTENTIAL ENERGY[hartree]    =         -0.687025973983E+03  
>> -0.687025973983E+03
>>  TOTAL KINETIC ENERGY[hartree]=          0.971145351369E+02   
>> 0.971145351369E+02
>>  QM KINETIC ENERGY[hartree]   =          0.891156598761E+02   
>> 0.891156598761E+02
>>  TOTAL TEMPERATURE[K]         =                    3579.168             
>> 3579.168
>>  QM TEMPERATURE[K]            =                  182138.939           
>> 182138.939
>>
>>  *******************************************************************************
>>
>>
>> and then after few steps the job is coming out with the following error
>>
>> *** ERROR in build_neighbor_lists  ***
>>  *
>>
>>
>>  *** GEOMETRY wrong or EMAX_SPLINE too small!  ***
>>
>> Note: Based on previous mailing list, increase in the EMAX_SPLINE value 
>> did not help me.
>> Any suggestions will be appreciated.
>>
>> regards,
>> Tarak
>> Molecular Simulation Lab.
>> JNCASR,
>> Bangalore, India
>>
>
>
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