[CP2K:2420] QM/MM input

Teodoro Laino teodor... at gmail.com
Tue Nov 24 18:11:51 CET 2009


Hi Caterina,

QM/MM fully periodic is definitely not the most trivial thing one can do.
I would suggest you first to try the non-periodic QM/MM coupling and 
check how the system behaves. Once you have
a better understanding you can try to move to the fully periodic one.

The reason why QM atoms twist and elongate too much may also be due to 
the QM setup. So better you try to isolate the source of this problem.

The line that specifies the fixed_atoms I think is too long: the list 
could be cut at the parsing of the input file.
The keyword LIST is repeatable. So better you use more of these keywords 
rather than having a single line with millions of numbers.

Regards
Teo

Caterina wrote:
> 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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