QMMM input file
cjor
chri... at gmail.com
Tue Jan 20 18:11:54 UTC 2015
Hello,
I'm trying to do a QM/MM simulation in CP2K of an iron(II) active site with
a dioxygen binding
reaction, in which the
overall charge of the QM part is -1, and spin multiplicity is 5 or 7
depending
on the spin-state of iron(II).
I am struggling with this. I attach my input file, and would like to hear
any experienced
user's comments on my setup.
My questions are:
(I) Which basis set and pseudopotential to use for Fe.
I've used the one that is recommended in the user forum
namely DZVP-MOLOPT-SR-GTH
(II) Do I need to define only the QM atom types, or both the
QM and MM?
(III) For the QM part, for the residues I've selected, I cut using the
link-atom
method, cutting between the alpha and beta carbons, thus effectively
describing my backbone with MM and my side-chain as QM. How many link
atoms is customary to use? I have used 6.
(IV) Does the command *&QM_KIND H** MM_INDEX *mean we define explicitly all
QM-treated
atom indices, and leave undefined all MM indices to be parsed in the pdb
file?
(IV) Is the default ensemble NVT, and if so, is NPT possible in CP2K?
*&FORCE_EVAL*
* METHOD QMMM*
* &DFT*
* basis_set_file_name BASIS_SET*
* potential_file_name POTENTIAL*
* charge -1*
* multiplicity 5*
* 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 par_all27_prot_lipid.inp*
* parmtype CHM*
* ei_scale14 1.0*
* vdw_scale14 1.0*
* &SPLINE*
* emax_spline 1.0*
* rcut_nb 12*
* &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 10 10 10*
* 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 1979*
* QM_INDEX 1981*
* QMMM_SCALE_FACTOR 0.0*
* RADIUS 0.80*
* &END LINK*
* &LINK*
* alpha 1.50*
* link_type IMOMM*
* MM_INDEX 2012*
* QM_INDEX 2014*
* QMMM_SCALE_FACTOR 0.0*
* RADIUS 0.80*
* &END LINK*
* &LINK*
* alpha 1.50*
* link_type IMOMM*
* MM_INDEX 2960*
* QM_INDEX 2962*
* QMMM_SCALE_FACTOR 0.0*
* RADIUS 0.80*
* &END LINK*
* &LINK*
* alpha 1.50*
* link_type IMOMM*
* MM_INDEX 3189*
* QM_INDEX 3200*
* QMMM_SCALE_FACTOR 0.0*
* RADIUS 0.80*
* &END LINK*
* &LINK*
* alpha 1.50*
* link_type IMOMM*
* MM_INDEX 3605*
* QM_INDEX 3607*
* QMMM_SCALE_FACTOR 0.0*
* RADIUS 0.80*
* &END LINK*
* &LINK*
* ALPHA 1.50*
* LINK_TYPE IMOMM*
* MM_INDEX 1918*
* QM_INDEX 1920*
* 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 OG2D2*
* RADIUS 0.77*
* &END MM_KIND*
* &MM_KIND CG205*
* RADIUS 0.77*
* &END MM_KIND*
* &MM_KIND OG2D3*
* RADIUS 0.77*
* &END MM_KIND*
* &MM_KIND CG321*
* RADIUS 0.77*
* &END MM_KIND*
* &MM_KIND HGA2*
* RADIUS 0.44*
* &END MM_KIND*
* &QM_KIND H*
* MM_INDEX 6 7 10 12 15 17 19 27 28 30 33 36 44 45 56 57 59 62 65 73
74 77 79 83 85 87 89 94 95 97 99 100 102 103 117 118 119 120 122 123*
* &END QM_KIND*
* &QM_KIND O*
* MM_INDEX 14 47 48 91 105 108 109 111 115 116 121 124 125*
* &END QM_KIND*
* &QM_KIND C*
* MM_INDEX 5 8 9 11 13 16 18 26 31 32 35 43 46 55 60 61 64 72 75 76
80 81 82 84 86 88 90 93 96 98 101 104 107 110 112 113 114*
* &END QM_KIND*
* &QM_KIND N*
* MM_INDEX 29 34 58 63 78 92*
* &END QM_KIND*
* &QM_KIND Fe*
* MM_INDEX 3781*
* &END QM_KIND*
* &END QMMM*
* &SUBSYS*
* &CELL*
* abc 80 80 80*
* 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*
* &KIND Fe*
* BASIS_SET DZVP-MOLOPT-SR-GTH*
* POTENTIAL DZVP-MOLOPT-SR-GTH*
* &END KIND*
* &TOPOLOGY*
* COORD_FILE_NAME file.pdb*
* COORDINATE pdb*
* CONN_FILE_NAME ionized.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 NPT*
* STEPS 2000*
* TIMESTEP 0.5*
* TEMPERATURE 298*
* &THERMOSTAT*
* &NOSE*
* &END NOSE*
* &END THERMOSTAT*
* &END MD*
*&END MOTION*
Regards
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