<div dir="ltr">Hello, <div><br></div><div>I'm trying to do a QM/MM simulation in CP2K of an iron(II) active site with a dioxygen binding</div><div>reaction, in which the </div><div>overall charge of the QM part is -1, and spin multiplicity is 5 or 7 depending</div><div>on the spin-state of iron(II).</div><div><br></div><div><br></div><div>I am struggling with this. I attach my input file, and would like to hear any experienced</div><div>user's comments on my setup. </div><div><br></div><div>My questions are:</div><div><br></div><div>(I) Which basis set and pseudopotential to use for Fe.</div><div>I've used the one that is recommended in the user forum</div><div>namely DZVP-MOLOPT-SR-GTH</div><div><br></div><div>(II) Do I need to define only the QM atom types, or both the</div><div>QM and MM? </div><div><br></div><div>(III) For the QM part, for the residues I've selected, I cut using the link-atom </div><div>method, cutting between the alpha and beta carbons, thus effectively </div><div>describing my backbone with MM and my side-chain as QM. How many link</div><div>atoms is customary to use? I have used 6. </div><div><br></div><div>(IV) Does the command <b>&QM_KIND H</b><b> MM_INDEX </b>mean we define explicitly all QM-treated </div><div>atom indices, and leave undefined all MM indices to be parsed in the pdb file?</div><div><br></div><div><br></div><div>(IV) Is the default ensemble NVT, and if so, is NPT possible in CP2K? </div><div><br></div><div><br></div><div><div><b><br></b></div><div><b>&FORCE_EVAL</b></div><div><b> METHOD QMMM</b></div><div><b> &DFT</b></div><div><b> basis_set_file_name BASIS_SET</b></div><div><b> potential_file_name POTENTIAL</b></div><div><b> charge -1</b></div><div><b> multiplicity 5</b></div><div><b> uks</b></div><div><b> &MGRID</b></div><div><b> commensurate</b></div><div><b> cutoff 280</b></div><div><b> &INTERPOLATOR</b></div><div><b> eps_r 1.0e-15</b></div><div><b> eps_x 1.0e-15</b></div><div><b> maxiter 100</b></div><div><b> &END INTERPOLATOR</b></div><div><b> &END MGRID</b></div><div><b> &QS</b></div><div><b> &END QS</b></div><div><b> &SCF</b></div><div><b> scf_guess atomic</b></div><div><b> max_scf 30</b></div><div><b> &OT</b></div><div><b> preconditioner FULL_SINGLE_INVERSE</b></div><div><b> minimizer DIIS</b></div><div><b> n_diis 7</b></div><div><b> &END</b></div><div><b> &OUTER_SCF</b></div><div><b> max_scf 5</b></div><div><b> eps_scf 1.0E-6</b></div><div><b> &END</b></div><div><b> &PRINT</b></div><div><b> &RESTART</b></div><div><b> add_last NUMERIC</b></div><div><b> backup_copies 0</b></div><div><b> &END</b></div><div><b> &RESTART_HISTORY OFF</b></div><div><b> &END</b></div><div><b> &END</b></div><div><b> &END SCF</b></div><div><b> &XC</b></div><div><b> &XC_FUNCTIONAL blyp</b></div><div><b> &END XC_FUNCTIONAL</b></div><div><b> &END XC</b></div><div><b> &END DFT</b></div><div><b> &MM</b></div><div><b> &FORCEFIELD</b></div><div><b> parm_file_name par_all27_prot_lipid.inp</b></div><div><b> parmtype CHM</b></div><div><b> ei_scale14 1.0</b></div><div><b> vdw_scale14 1.0</b></div><div><b> &SPLINE</b></div><div><b> emax_spline 1.0</b></div><div><b> rcut_nb 12</b></div><div><b> &END SPLINE</b></div><div><b> &END FORCEFIELD</b></div><div><b> &POISSON</b></div><div><b> &EWALD</b></div><div><b> ewald_type SPME</b></div><div><b> alpha 0.44</b></div><div><b> gmax 81</b></div><div><b> &END EWALD</b></div><div><b> &END POISSON</b></div><div><b> &END MM</b></div><div><b><br></b></div><div><b><br></b></div><div><b> &QMMM</b></div><div><b> nocompatibility</b></div><div><b> ecoupl GAUSS</b></div><div><b> use_geep_lib 10</b></div><div><b> nocenter0</b></div><div><b> &WALLS</b></div><div><b> type reflective</b></div><div><b> &END WALLS</b></div><div><b> &CELL</b></div><div><b> abc 10 10 10</b></div><div><b> periodic xyz</b></div><div><b> &END CELL</b></div><div><b> &INTERPOLATOR</b></div><div><b> eps_r 1.0e-15</b></div><div><b> eps_x 1.0e-15</b></div><div><b> maxiter 100</b></div><div><b> &END INTERPOLATOR</b></div><div><b> &PERIODIC</b></div><div><b> gmax 0.5</b></div><div><b> &MULTIPOLE</b></div><div><b> analytical_gterm</b></div><div><b> ewald_precision 1.00000000E-06</b></div><div><b> ngrids 50 50 50</b></div><div><b> rcut 40</b></div><div><b> &END MULTIPOLE</b></div><div><b> &END PERIODIC</b></div><div><b> &PRINT</b></div><div><b> &PERIODIC_INFO</b></div><div><b> &END PERIODIC_INFO</b></div><div><b> &POTENTIAL</b></div><div><b> &END POTENTIAL</b></div><div><b> &END PRINT</b></div><div><b> &LINK</b></div><div><b> alpha 1.50</b></div><div><b> link_type IMOMM</b></div><div><b> MM_INDEX 1979</b></div><div><b> QM_INDEX 1981</b></div><div><b> QMMM_SCALE_FACTOR 0.0</b></div><div><b> RADIUS 0.80</b></div><div><b> &END LINK</b></div><div><b> &LINK</b></div><div><b> alpha 1.50</b></div><div><b> link_type IMOMM</b></div><div><b> MM_INDEX 2012</b></div><div><b> QM_INDEX 2014</b></div><div><b> QMMM_SCALE_FACTOR 0.0</b></div><div><b> RADIUS 0.80</b></div><div><b> &END LINK</b></div><div><b> &LINK</b></div><div><b> alpha 1.50</b></div><div><b> link_type IMOMM</b></div><div><b> MM_INDEX 2960</b></div><div><b> QM_INDEX 2962</b></div><div><b> QMMM_SCALE_FACTOR 0.0</b></div><div><b> RADIUS 0.80</b></div><div><b> &END LINK</b></div><div><b> &LINK</b></div><div><b> alpha 1.50</b></div><div><b> link_type IMOMM</b></div><div><b> MM_INDEX 3189</b></div><div><b> QM_INDEX 3200</b></div><div><b> QMMM_SCALE_FACTOR 0.0</b></div><div><b> RADIUS 0.80</b></div><div><b> &END LINK</b></div><div><b> &LINK</b></div><div><b> alpha 1.50</b></div><div><b> link_type IMOMM</b></div><div><b> MM_INDEX 3605</b></div><div><b> QM_INDEX 3607</b></div><div><b> QMMM_SCALE_FACTOR 0.0</b></div><div><b> RADIUS 0.80</b></div><div><b> &END LINK</b></div><div><b> &LINK</b></div><div><b> ALPHA 1.50</b></div><div><b> LINK_TYPE IMOMM</b></div><div><b> MM_INDEX 1918</b></div><div><b> QM_INDEX 1920</b></div><div><b> QMMM_SCALE_FACTOR 0.0</b></div><div><b> RADIUS 0.80</b></div><div><b> &END LINK</b></div><div><b><br></b></div><div><b> &MM_KIND NH3</b></div><div><b> RADIUS 0.71</b></div><div><b> &END MM_KIND</b></div><div><b><br></b></div><div><b> &MM_KIND HC</b></div><div><b> RADIUS 0.32</b></div><div><b> &END MM_KIND</b></div><div><b><br></b></div><div><b> &MM_KIND CT1</b></div><div><b> RADIUS 0.77</b></div><div><b> &END MM_KIND</b></div><div><b><br></b></div><div><b> &MM_KIND HB</b></div><div><b> RADIUS 0.30</b></div><div><b> &END MM_KIND</b></div><div><b><br></b></div><div><b> &MM_KIND CT3</b></div><div><b> RADIUS 0.78</b></div><div><b> &END MM_KIND</b></div><div><b><br></b></div><div><b> &MM_KIND HA</b></div><div><b> RADIUS 0.32</b></div><div><b> &END MM_KIND</b></div><div><b><br></b></div><div><b> &MM_KIND C</b></div><div><b> RADIUS 0.69</b></div><div><b> &END MM_KIND</b></div><div><b><br></b></div><div><b> &MM_KIND O</b></div><div><b> RADIUS 0.52</b></div><div><b> &END MM_KIND</b></div><div><b><br></b></div><div><b> &MM_KIND NH1</b></div><div><b> RADIUS 0.65</b></div><div><b> &END MM_KIND</b></div><div><b><br></b></div><div><b> &MM_KIND H</b></div><div><b> RADIUS 0.34</b></div><div><b> &END MM_KIND</b></div><div><b><br></b></div><div><b> &MM_KIND OH1</b></div><div><b> RADIUS 0.65</b></div><div><b> &END MM_KIND</b></div><div><b><br></b></div><div><b> &MM_KIND CT2</b></div><div><b> RADIUS 0.78</b></div><div><b> &END MM_KIND</b></div><div><b><br></b></div><div><b> &MM_KIND SM</b></div><div><b> RADIUS 1.02</b></div><div><b> &END MM_KIND</b></div><div><b><br></b></div><div><b> &MM_KIND CC</b></div><div><b> RADIUS 0.73</b></div><div><b> &END MM_KIND</b></div><div><b><br></b></div><div><b> &MM_KIND OC</b></div><div><b> RADIUS 0.56</b></div><div><b> &END MM_KIND</b></div><div><b><br></b></div><div><b> &MM_KIND NC2</b></div><div><b> RADIUS 0.69</b></div><div><b> &END MM_KIND</b></div><div><b><br></b></div><div><b> &MM_KIND NH2</b></div><div><b> RADIUS 0.66</b></div><div><b> &END MM_KIND</b></div><div><b><br></b></div><div><b> &MM_KIND CA</b></div><div><b> RADIUS 0.70</b></div><div><b> &END MM_KIND</b></div><div><b><br></b></div><div><b> &MM_KIND HP</b></div><div><b> RADIUS 0.37</b></div><div><b> &END MM_KIND</b></div></div><div><div><b> &MM_KIND OG2D2</b></div><div><b> RADIUS 0.77</b></div><div><b> &END MM_KIND</b></div><div><b><br></b></div><div><b> &MM_KIND CG205</b></div><div><b> RADIUS 0.77</b></div><div><b> &END MM_KIND</b></div><div><b><br></b></div><div><b> &MM_KIND OG2D3</b></div><div><b> RADIUS 0.77</b></div><div><b> &END MM_KIND</b></div><div><b><br></b></div><div><b> &MM_KIND CG321</b></div><div><b> RADIUS 0.77</b></div><div><b> &END MM_KIND</b></div><div><b><br></b></div><div><b> &MM_KIND HGA2</b></div><div><b> RADIUS 0.44</b></div><div><b> &END MM_KIND</b></div><div><b><br></b></div><div><b><br></b></div><div><b> &QM_KIND H</b></div><div><b> 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</b></div><div><b> &END QM_KIND</b></div><div><b> &QM_KIND O</b></div><div><b> MM_INDEX 14 47 48 91 105 108 109 111 115 116 121 124 125</b></div><div><b> &END QM_KIND</b></div><div><b> &QM_KIND C</b></div><div><b> 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</b></div><div><b> &END QM_KIND</b></div><div><b> &QM_KIND N</b></div><div><b> MM_INDEX 29 34 58 63 78 92</b></div><div><b> &END QM_KIND</b></div><div><b> &QM_KIND Fe</b></div><div><b> MM_INDEX 3781</b></div><div><b> &END QM_KIND</b></div><div><b><br></b></div><div><b><br></b></div><div><b> &END QMMM</b></div><div><b> &SUBSYS</b></div><div><b> &CELL</b></div><div><b> abc 80 80 80</b></div><div><b> periodic xyz</b></div><div><b> &END CELL</b></div><div><b> &KIND H</b></div><div><b> BASIS_SET DZVP-GTH-BLYP</b></div><div><b> POTENTIAL GTH-BLYP-q1</b></div><div><b> &END KIND</b></div><div><b> &KIND O</b></div><div><b> BASIS_SET DZVP-GTH-BLYP</b></div><div><b> POTENTIAL GTH-BLYP-q6</b></div><div><b> &END KIND</b></div><div><b> &KIND N</b></div><div><b> BASIS_SET DZVP-GTH-BLYP</b></div><div><b> POTENTIAL GTH-BLYP-q5</b></div><div><b> &END KIND</b></div><div><b> &KIND C</b></div><div><b> BASIS_SET DZVP-GTH-BLYP</b></div><div><b> POTENTIAL GTH-BLYP-q4</b></div><div><b> &END KIND</b></div><div><b> &KIND Fe</b></div><div><b> BASIS_SET DZVP-MOLOPT-SR-GTH</b></div><div><b> POTENTIAL DZVP-MOLOPT-SR-GTH</b></div><div><b> &END KIND</b></div><div><b><br></b></div><div><b> &TOPOLOGY</b></div><div><b> COORD_FILE_NAME file.pdb</b></div><div><b> COORDINATE pdb</b></div><div><b> CONN_FILE_NAME ionized.psf</b></div><div><b> CONN_FILE_FORMAT upsf</b></div><div><b> &END TOPOLOGY</b></div><div><b> &END SUBSYS</b></div><div><b>&END FORCE_EVAL</b></div><div><b>&GLOBAL</b></div><div><b> PROJECT md-nvt</b></div><div><b> RUN_TYPE md</b></div><div><b> PRINT_LEVEL medium</b></div><div><b>&END GLOBAL</b></div><div><b>#&MOTION</b></div><div><b># &CONSTRAINT</b></div><div><b># &FIXED_ATOMS</b></div><div><b># list 2415 4645 4646 4647 4648 4649 4650</b></div><div><b>#4651 4652 4653 4654 4655 4656 4657 4658</b></div><div><b>#4659 4660 4661 4662 4663 4664 4665 4666</b></div><div><b>#4667 4668 4669 4670 4671 4672 4673 4674</b></div><div><b>#4675 4676 4677 4678 4679 4680 4681 4682</b></div><div><b>#4683 4684 4685 4686 4687 4688 4689 4690</b></div><div><b>#4691 4692 4693 4694 4695 4696 4697 4698</b></div><div><b>#4699 4700 4701 4702 4703 4704 4705 4706</b></div><div><b>#4707 4708 4709 4710 4711 4712 4713 4714</b></div><div><b>#4715 4716 4717 4718 4721 4722</b></div><div><b># &END FIXED_ATOMS</b></div><div><b># &END CONSTRAINT</b></div><div><b> &PRINT</b></div><div><b> &TRAJECTORY</b></div><div><b> format dcd</b></div><div><b> &END TRAJECTORY</b></div><div><b> &END PRINT</b></div><div><b> &MD</b></div><div><b> ENSEMBLE NPT</b></div><div><b> STEPS 2000</b></div><div><b> TIMESTEP 0.5</b></div><div><b> TEMPERATURE 298</b></div><div><b> &THERMOSTAT</b></div><div><b> &NOSE</b></div><div><b> &END NOSE</b></div><div><b> &END THERMOSTAT</b></div><div><b> &END MD</b></div><div><b>&END MOTION</b></div></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div>Regards</div><div><br></div></div>