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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