QM/MM high temperature
tarak karmakar
tarak... at gmail.com
Wed Feb 26 05:58:56 UTC 2014
Any suggestions?
On Fri, Feb 21, 2014 at 2:00 PM, tarak karmakar <tarak... at gmail.com>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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