QM/MM high temperature

tarak karmakar tarak... at gmail.com
Fri Feb 21 08:30:50 UTC 2014


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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