QM/MM input

Caterina bern... at libero.it
Tue Nov 24 17:55:18 CET 2009


Dear CP2K experts,
I would like to setup QM/MM calculations on a large system with PBC
using CP2K code. I have already done a classical MD equilibration with
NAMD and a QM/MM optimization using a different QM/MM code. Now I
would like to start from the optimized structure to perform a QM/MM
dynamics (NVT ensamble). After reading some papers on CP2K, the on-
line manual, the mailing list and regtests, I have written the
following input. I would be grateful if you could give a look at my
input and tell me if there are any errors, particularly relative to
the QM/MM electrostatic coupling. The following input works (I mean it
gives me no error messages), but I noticed a strange behavior of the
QM atoms that twist and elongate too much.
Any help is very welcome.

Thanks

Caterina


&FORCE_EVAL
  METHOD QMMM
  &DFT
    basis_set_file_name BASIS_SET
    potential_file_name POTENTIAL
    charge 0
    multiplicity 2
    uks
    &MGRID
      commensurate
      cutoff 280
    &INTERPOLATOR
      eps_r 1.0e-15
      eps_x 1.0e-15
      maxiter 100
    &END INTERPOLATOR
    &END MGRID
    &QS
    &END QS
    &SCF
       scf_guess atomic
       max_scf 30
       &OT
         preconditioner FULL_SINGLE_INVERSE
         minimizer DIIS
         n_diis 7
       &END
       &OUTER_SCF
         max_scf 5
         eps_scf 1.0E-6
       &END
       &PRINT
         &RESTART
            add_last NUMERIC
            backup_copies 0
         &END
         &RESTART_HISTORY OFF
         &END
       &END
    &END SCF
    &XC
      &XC_FUNCTIONAL blyp
      &END XC_FUNCTIONAL
    &END XC
  &END DFT
  &MM
    &FORCEFIELD
      parm_file_name charmm.pot
      parmtype CHM
      ei_scale14 1.0
      vdw_scale14 1.0
      &SPLINE
        emax_spline 1.0
      &END SPLINE
    &END FORCEFIELD
    &POISSON
      &EWALD
        ewald_type SPME
        alpha 0.44
        gmax 81
      &END EWALD
    &END POISSON
  &END MM
  &QMMM
    nocompatibility
    ecoupl GAUSS
    use_geep_lib 10
    nocenter0
    &WALLS
      type reflective
    &END WALLS
    &CELL
      abc 8.0 8.0 12.0
      periodic xyz
    &END CELL
    &INTERPOLATOR
      eps_r 1.0e-15
      eps_x 1.0e-15
      maxiter 100
    &END INTERPOLATOR
    &PERIODIC
      gmax 0.5
      &MULTIPOLE
        analytical_gterm
        ewald_precision 1.00000000E-06
        ngrids 50 50 50
        rcut 40
      &END MULTIPOLE
    &END PERIODIC
    &PRINT
      &PERIODIC_INFO
      &END PERIODIC_INFO
      &POTENTIAL
      &END POTENTIAL
    &END PRINT
    &LINK
      alpha 1.50
      link_type IMOMM
      MM_INDEX 2306
      QM_INDEX 2318
      QMMM_SCALE_FACTOR 0.0
      RADIUS 0.80
    &END LINK
    &LINK
      ALPHA 1.50
      LINK_TYPE IMOMM
      MM_INDEX 2346
      QM_INDEX 2344
      QMMM_SCALE_FACTOR 0.0
      RADIUS 0.80
    &END LINK
    &LINK
      ALPHA 1.50
      LINK_TYPE IMOMM
      MM_INDEX 3511
      QM_INDEX 3513
      QMMM_SCALE_FACTOR 0.0
      RADIUS 0.80
    &END LINK

    &MM_KIND NH3
      RADIUS 0.71
    &END MM_KIND

    &MM_KIND HC
      RADIUS 0.32
    &END MM_KIND

    &MM_KIND CT1
      RADIUS 0.77
    &END MM_KIND

    &MM_KIND HB
      RADIUS 0.30
    &END MM_KIND

    &MM_KIND CT3
      RADIUS 0.78
    &END MM_KIND

    &MM_KIND HA
      RADIUS 0.32
    &END MM_KIND

    &MM_KIND C
      RADIUS 0.69
    &END MM_KIND

    &MM_KIND O
      RADIUS 0.52
    &END MM_KIND

    &MM_KIND NH1
      RADIUS 0.65
    &END MM_KIND

    &MM_KIND H
      RADIUS 0.34
    &END MM_KIND

    &MM_KIND OH1
      RADIUS 0.65
    &END MM_KIND

    &MM_KIND CT2
      RADIUS 0.78
    &END MM_KIND

    &MM_KIND SM
      RADIUS 1.02
    &END MM_KIND

    &MM_KIND CC
      RADIUS 0.73
    &END MM_KIND

    &MM_KIND OC
      RADIUS 0.56
    &END MM_KIND

    &MM_KIND NC2
      RADIUS 0.69
    &END MM_KIND

    &MM_KIND NH2
      RADIUS 0.66
    &END MM_KIND

    &MM_KIND CA
      RADIUS 0.70
    &END MM_KIND

    &MM_KIND HP
      RADIUS 0.37
    &END MM_KIND

    &MM_KIND N
      RADIUS 0.64
    &END MM_KIND

    &MM_KIND CP3
      RADIUS 0.79
    &END MM_KIND

    &MM_KIND CP1
      RADIUS 0.77
    &END MM_KIND

    &MM_KIND CP2
      RADIUS 0.77
    &END MM_KIND

    &MM_KIND CD
      RADIUS 0.74
    &END MM_KIND

    &MM_KIND OB
      RADIUS 0.49
    &END MM_KIND

    &MM_KIND NR2
      RADIUS 0.65
    &END MM_KIND

    &MM_KIND CPH1
      RADIUS 0.70
    &END MM_KIND

    &MM_KIND CPH2
      RADIUS 0.67
    &END MM_KIND

    &MM_KIND HR1
      RADIUS 0.40
    &END MM_KIND

    &MM_KIND NR1
      RADIUS 0.69
    &END MM_KIND

    &MM_KIND HR3
      RADIUS 0.39
    &END MM_KIND

    &MM_KIND NR3
      RADIUS 0.66
    &END MM_KIND

    &MM_KIND HR2
      RADIUS 0.40
    &END MM_KIND

    &MM_KIND S
      RADIUS 1.04
    &END MM_KIND

    &MM_KIND CY
      RADIUS 0.72
    &END MM_KIND

    &MM_KIND NY
      RADIUS 0.66
    &END MM_KIND

    &MM_KIND CPT
      RADIUS 0.70
    &END MM_KIND

    &MM_KIND FE
      RADIUS 1.58
    &END MM_KIND

    &MM_KIND NPH
      RADIUS 0.58
    &END MM_KIND

    &MM_KIND CPA
      RADIUS 0.60
    &END MM_KIND

    &MM_KIND CPB
      RADIUS 0.71
    &END MM_KIND

    &MM_KIND CPM
      RADIUS 1.12
    &END MM_KIND




    &QM_KIND H
      MM_INDEX 2321 2323 2325 2326 2329 2331 2335 2337 2339 2341 2345
3514 3515 3517 3518
    &END QM_KIND
    &QM_KIND O
      MM_INDEX 2319 2343 3520 3521
    &END QM_KIND
    &QM_KIND C
      MM_INDEX 2318 2322 2324 2327 2328 2332 2333 2334 2336 2338 2340
2342 3513 3516 3519
    &END QM_KIND
    &QM_KIND N
      MM_INDEX 2320 2330 2344
    &END QM_KIND
  &END QMMM
  &SUBSYS
    &CELL
      abc 69.0 80.0 76.0
      periodic xyz
    &END CELL
    &KIND H
      BASIS_SET DZVP-GTH-BLYP
      POTENTIAL GTH-BLYP-q1
    &END KIND
    &KIND O
      BASIS_SET DZVP-GTH-BLYP
      POTENTIAL GTH-BLYP-q6
    &END KIND
    &KIND N
      BASIS_SET DZVP-GTH-BLYP
      POTENTIAL GTH-BLYP-q5
    &END KIND
    &KIND C
      BASIS_SET DZVP-GTH-BLYP
      POTENTIAL GTH-BLYP-q4
    &END KIND
    &TOPOLOGY
      COORD_FILE_NAME file.pdb
      COORDINATE pdb
      CONN_FILE_NAME file.psf
      CONN_FILE_FORMAT upsf
    &END TOPOLOGY
  &END SUBSYS
&END FORCE_EVAL
&GLOBAL
  PROJECT md-nvt
  RUN_TYPE md
  PRINT_LEVEL medium
&END GLOBAL
&MOTION
  &CONSTRAINT
    &FIXED_ATOMS
  list 2415     4645    4646    4647    4648    4649    4650
4651    4652    4653    4654    4655    4656    4657    4658
4659    4660    4661    4662    4663    4664    4665    4666
4667    4668    4669    4670    4671    4672    4673    4674
4675    4676    4677    4678    4679    4680    4681    4682
4683    4684    4685    4686    4687    4688    4689    4690
4691    4692    4693    4694    4695    4696    4697    4698
4699    4700    4701    4702    4703    4704    4705    4706
4707    4708    4709    4710    4711    4712    4713    4714
4715    4716    4717    4718    4721    4722
    &END FIXED_ATOMS
  &END CONSTRAINT
  &PRINT
     &TRAJECTORY
       format dcd
     &END TRAJECTORY
  &END PRINT
  &MD
    ENSEMBLE NVT
    STEPS 2000
    TIMESTEP 0.5
    TEMPERATURE 298
    &THERMOSTAT
      &NOSE
      &END NOSE
    &END THERMOSTAT
  &END MD
&END MOTION



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