NAMD equil CP2K QM/MM

[tarak karmakar]

Dear All,

I'm trying to perform a QM/MM simulation in CP2K by taking the well
equilibrated (seeing the tot_eng, pot_eng, temperature) configuration
obtained from classical simulation in NAMD with charmm force field.

In QM/MM input file I use the simulation box lengths and its center of mass
from the .xst file (NAMD) for a selected frame. The QM/MM input file 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
     SCF_GUESS ATOMIC                 ##atomic,restart,random,or core
     EPS_SCF 1.0e-6
     MAX_SCF 250
     &OUTER_SCF
        MAX_SCF                10
     &END OUTER_SCF


      &OT ON

    PRECOND_SOLVER INVERSE_CHOLESKY
    PRECONDITIONER FULL_KINETIC

    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 80 80 80
        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

    &WALLS
      TYPE REFLECTIVE
       WALL_SKIN 0.5 0.5 0.5
    &END WALLS

   &CELL
     ABC [angstrom] 20.0 20.0 20.0
     PERIODIC XYZ
   &END CELL

  &PERIODIC
      GMAX 0.11
     &MULTIPOLE
        EWALD_PRECISION 0.000001
        RCUT 11.0
        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 26 252 253 306 307 957 958 984 985
1041 1042 1044 1045 1518 1519 1581 1582 1845 1846 2013 2014 2073 2074 2304
2305 2538 2539 3246 3247 3480 3481 4089 4090 4125 4126 4131 4132 4974 4975
5262 5263 5442 5443 5481 5482 5655 5656
    &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 34 251 305 956 983 1040 1043
1517 1580 1844 2012 2072 2303 2537 3245 3479 4088 4124 4130 4973 5261 5441
5480 5654
    &END QM_KIND
    &QM_KIND P
      MM_INDEX 28
    &END QM_KIND
  &END QMMM
#...........................................................

  &SUBSYS
    &CELL
      ABC [angstrom] 37.9474 37.8769 37.9203
      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_400step.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 4
        YOSHIDA 9
        TIMECON 1000
        MTS 2
      &END NOSE
    &END THERMOSTAT

    &PRINT
      &ENERGY
        &EACH
          MD 1
        &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 1
      &END EACH
    &END TRAJECTORY

    &VELOCITIES OFF
          LOG_PRINT_KEY T
          FORMAT XYZ
          UNIT angstrom
          &EACH
            MD 10
          &END EACH
          ADD_LAST NUMERIC
    &END VELOCITIES

    &FORCES OFF
    &END FORCES
  &END PRINT
&END MOTION
#....................END......................................


My QM system comprises of an organic molecule and 23 quantum water
molecules in a QM box of 20x20x20.

While running the simulation, it showing very high temperature and then
getting terminated with error



******************************************************************
 *** ERROR in build_neighbor_lists (MODULE fist_neighbor_lists) ***
 ******************************************************************

 *** GEOMETRY wrong or EMAX_SPLINE too small! ***

 *** Program stopped at line number 623 of MODULE fist_neighbor_lists ***

 ===== Routine Calling Stack =====

            7 build_neighbor_lists
            6 build_fist_neighbor_lists
            5 list_control
            4 fist_force_control
            3 velocity_verlet
            2 qs_mol_dyn_low
            1 CP2K
 CP2K| Abnormal program termination, stopped by process number 2
rank 2 in job 1  cauvery_33033   caused collective abort of all ranks
  exit status of rank 2: return code 1

I don't know why it is telling the geometry is wrong.



Tarak
Molecular Simulations Lab.
JNCASR
Bangalore, India
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20140314/827c0a75/attachment.htm>