.. tip:: All input files can be downloaded: :download:`Files `. xtb ====== .. contents:: :local: This keyword controls the xTB calculation options. Options ------------ .. contents:: :local: .. option:: chrg .. list-table:: :stub-columns: 1 :widths: 5 20 * - Value - An integer * - Default - ``0`` The total charge of the system. .. option:: uhf .. list-table:: :stub-columns: 1 :widths: 5 20 * - Value - An integer * - Default - ``0`` The number of unpaired electrons. .. option:: gfn .. list-table:: :stub-columns: 1 :widths: 5 20 * - Value - ``1`` The GFN1-xTB Hamiltonian. * - - ``2`` The GFN2-xTB Hamiltonian. * - Default - ``2`` Define the xTB Hamiltonian type. .. option:: gbsa .. list-table:: :stub-columns: 1 :widths: 5 20 * - Value - ``H2O`` * - - ``Acetone`` * - - ``Acetonitrile`` * - - ``Benzene`` * - - ``CH2Cl2`` * - - ``CHCl3`` * - - ``CS2`` * - - ``DMSO`` * - - ``Ether`` * - - ``Hexane`` * - - ``Toluene`` * - - ``THF`` * - Default - None The solvent name. If it is not given, the xTB is calculated in the gas phase. Otherwise, generalized Born model will be used to consider solvent effects. .. option:: etemp .. list-table:: :stub-columns: 1 :widths: 5 20 * - Value - A real number * - Default - ``300`` The electronic temperature in Kelvin. .. option:: vparam .. list-table:: :stub-columns: 1 :widths: 5 20 * - Value - A file name for the xTB parameter file. * - Default - None If not given, the default parameters stored internally in Qbics will be used. If a file name (path can be included) is given, the xTB calculation will use the parameters in this file. Theoretical Background -------------------------------- xTB is a powerful semiempirical quantum chemical method proposed by Stefan Grimme. It has been designed for the purpose of facilitating rapid and accurate electronic structure calculations of large molecular systems (approximately 1000 atoms). It can be used to rapidly give good initial guess for DFT calculations. xTB has several Hamiltonians. Qbics supports GFN-1 and GFN-2. It seems that: - GFN1-xTB: When a system contains **metal cluster**-like structures, this is better. - GFN2-xTB: For most organic molecules with no or a few metal atoms. To consider solvent effects, one can use ``gbsa``. xTB can also work with CHARMM force field, i.e., xTB/MM method. This is a powerful way to study large, complicated systems. For all features of xTB method, please refer to the `xTB manual `_. Input Examples -------------------- In all examples below, you can change ``opt`` to ``md`` to do molecular dynamics. Example: Geometry Optimization by GFN2-xTB for Cantharidin ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Perform geometry optimization by GFN2-xTb for an organic molecule cantharidin: .. code-block:: bash :linenos: :caption: xtb-1.inp xtb chrg 0 gfn 2 # GFN2-xTB. end # Cantharidin mol C 1.39900 0.71500 1.06800 C 1.92100 -0.06900 -0.14800 C 0.78600 -0.69800 -1.04400 C 0.13800 -2.16200 -0.87800 C 1.29700 -3.05700 -0.50500 C 2.44700 -2.21000 -1.00400 O 1.70700 -1.35300 -1.91200 C 2.98300 -1.16300 -0.03500 C 3.42500 -1.73000 1.31300 C 4.18700 -0.54700 -0.69400 O 5.29000 -1.08800 -0.78200 O 3.91700 0.65900 -1.20900 C 2.61300 0.98300 -0.99400 O 2.10200 2.01700 -1.40000 H 0.94400 0.07300 1.82400 H 0.61300 1.41400 0.73300 H 2.16400 1.34500 1.53700 H 0.05600 -0.55500 -0.22800 H -0.28600 -2.46400 -1.85300 H -0.70400 -2.25200 -0.17500 H 1.22700 -4.00600 -1.04600 H 1.31500 -3.28300 0.56100 H 3.20900 -2.78100 -1.54000 H 2.64400 -2.28900 1.83300 H 3.79300 -0.95400 1.99200 H 4.26100 -2.43200 1.16600 end task opt xtb end Example: Geometry Optimization by GFN1-xTB for Co\ :sub:`6`\ Te\ :sub:`8`\ (P(Et)\ :sub:`3`\ )\ :sub:`6` ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Perform geometry optimization by GFN1-xTB for a quantum dot Co\ :sub:`6`\ Te\ :sub:`8`\ (P(Et)\ :sub:`3`\ )\ :sub:`6`. For such inorganic systems, GFN2-xTB may not converge. .. code-block:: bash :linenos: :caption: xtb-2.inp xtb chrg 0 gfn 1 # GFN1-xTB. Do you want to try GFN2-xTB? end # Quantum dot: Co6Te8(P(Et)3)6 mol Co 0.07482 0.19972 2.25274 Co -0.57236 2.10842 -0.12184 Co 2.14275 0.01139 -0.00690 Co 0.05260 -2.18506 -0.00075 Co -0.03312 0.01926 -2.21965 Co -2.27062 -0.26857 0.13243 Te -1.92498 1.48104 1.75344 Te 1.51638 1.80079 -1.53651 Te -1.62601 -1.71313 -1.72073 Te -1.37710 -1.68992 1.91428 Te 1.61324 -1.60191 1.77284 Te -2.00357 1.32469 -1.66240 Te 1.66650 -1.63285 -1.74916 Te 1.57938 1.94121 1.38532 P -4.02850 -1.49064 0.26273 C -5.19829 -1.41084 -1.21441 H -4.71377 -1.92702 -2.04886 H -6.13262 -1.93467 -0.99467 C -5.52751 0.01728 -1.64482 H -6.14156 0.00324 -2.54679 H -6.07317 0.54663 -0.86250 H -4.61066 0.57223 -1.85793 C -5.30003 -1.10968 1.60881 H -5.85560 -0.21489 1.31212 H -6.02467 -1.92631 1.68168 C -4.67909 -0.85880 2.97985 H -5.45790 -0.66760 3.72007 H -4.08936 -1.71732 3.30379 H -4.01919 0.01101 2.93660 C -3.88381 -3.34584 0.48895 H -3.69815 -3.52421 1.55200 H -2.98357 -3.67170 -0.04002 C -5.05361 -4.21895 0.03691 H -4.86097 -5.25352 0.32700 H -5.98965 -3.90442 0.49944 H -5.17056 -4.18666 -1.04614 P 4.26310 -0.30746 0.15884 C 5.20849 0.27270 -1.36436 H 4.75167 1.21294 -1.69163 H 6.25460 0.48490 -1.12936 C 5.15727 -0.72993 -2.51672 H 5.46512 -0.25078 -3.44736 H 5.81933 -1.57520 -2.32685 H 4.14177 -1.11524 -2.64233 C 5.11814 -1.95972 0.40905 H 4.65430 -2.67193 -0.28084 H 6.17155 -1.88201 0.12313 C 5.02841 -2.52709 1.82421 H 5.41753 -3.54657 1.84052 H 5.60186 -1.92517 2.52917 H 3.98817 -2.54672 2.15600 C 5.07249 0.73925 1.49299 H 4.67423 0.39189 2.45186 H 4.69613 1.75999 1.36590 C 6.59882 0.77674 1.57721 H 6.89665 1.35016 2.45694 H 7.01872 -0.22476 1.66541 H 7.03038 1.25623 0.69893 P 0.54020 0.66347 -4.18625 C 0.22564 2.40032 -4.82496 H 0.71085 3.09306 -4.13064 H 0.69956 2.53727 -5.80137 C -1.25205 2.77005 -4.94545 H -1.35213 3.83547 -5.15929 H -1.73005 2.21033 -5.75002 H -1.77854 2.55103 -4.01396 C -0.31031 -0.32739 -5.55031 H -1.38586 -0.13635 -5.48194 H 0.01101 0.00196 -6.54210 C -0.07813 -1.83035 -5.40257 H -0.63237 -2.37433 -6.16909 H 0.97995 -2.07651 -5.49904 H -0.42183 -2.16791 -4.42187 C 2.34305 0.47110 -4.66339 H 2.65871 -0.51529 -4.31013 H 2.90238 1.20335 -4.07212 C 2.73771 0.61134 -6.13325 H 3.82165 0.51779 -6.22187 H 2.28001 -0.16835 -6.74157 H 2.44775 1.58156 -6.53622 P 0.62497 1.10725 4.12138 C 2.39189 1.12488 4.75495 H 2.99045 1.67998 4.02630 H 2.45236 1.66544 5.70425 C 2.99908 -0.26481 4.94187 H 4.06777 -0.18045 5.14607 H 2.52854 -0.78692 5.77566 H 2.86297 -0.86705 4.04081 C -0.20941 0.28666 5.60490 H 0.15369 -0.74420 5.66370 H 0.07196 0.77828 6.54013 C -1.73060 0.25398 5.47187 H -2.17355 -0.26257 6.32492 H -2.14306 1.26238 5.42400 H -2.01420 -0.27566 4.55989 C 0.18744 2.91028 4.39005 H -0.80673 3.06756 3.95946 H 0.88329 3.49228 3.77726 C 0.19716 3.46228 5.81507 H 0.01322 4.53785 5.78327 H -0.58383 3.00325 6.42068 H 1.15764 3.29671 6.30321 P 0.50037 -4.23165 -0.45649 C 0.33638 -4.95275 -2.18024 H 0.88223 -4.28949 -2.85878 H 0.82383 -5.93134 -2.22239 C -1.09935 -5.10086 -2.67831 H -1.09940 -5.40811 -3.72540 H -1.64199 -5.84739 -2.09777 H -1.62712 -4.14741 -2.59715 C -0.42694 -5.55682 0.51882 H -1.48401 -5.50017 0.24082 H -0.08115 -6.55916 0.25173 C -0.31641 -5.35550 2.02886 H -0.92092 -6.09745 2.55307 H 0.71702 -5.44947 2.36437 H -0.67723 -4.36005 2.30237 C 2.28540 -4.69974 -0.10975 H 2.56512 -4.22430 0.83575 H 2.88463 -4.21217 -0.88607 C 2.66107 -6.17949 -0.04535 H 3.74212 -6.26881 0.07682 H 2.18351 -6.67142 0.80162 H 2.37807 -6.70546 -0.95721 P -1.88362 3.80220 0.05043 C -3.72133 3.80113 0.43439 H -3.92611 2.89184 1.00638 H -3.95713 4.64298 1.09168 C -4.66286 3.84410 -0.76765 H -5.68683 3.66404 -0.43496 H -4.62838 4.81311 -1.26529 H -4.39293 3.06880 -1.48575 C -1.85215 4.95783 -1.44558 H -2.32560 4.43432 -2.28107 H -2.43731 5.86170 -1.25698 C -0.43388 5.34449 -1.86016 H -0.45831 5.92448 -2.78423 H 0.05377 5.94199 -1.08916 H 0.16816 4.44750 -2.03047 C -1.28938 4.97422 1.41176 H -0.19434 4.95693 1.40891 H -1.60040 4.51594 2.35618 C -1.76235 6.42709 1.38328 H -1.44247 6.92890 2.29841 H -1.33556 6.96411 0.53662 H -2.84893 6.49209 1.32206 end task opt xtb end Example: Geometry Optimization by GFN2-xTB for Avibactam in Implicit Solvent ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Perform geometry optimization by GFN2-xTB for an organic anion in implicit DMSO solvent: .. code-block:: bash :linenos: :caption: xtb-3.inp xtb chrg -1 # The charge is set here. gfn 2 gbsa DMSO # This is in the list of xtb/gbsa item. end # Avibactam anion. mol N 1.83500 1.56700 0.16500 C 2.12100 0.23900 0.16900 O 1.81100 -0.44100 -0.81200 C 2.91300 -0.26000 1.37900 C 3.39800 -1.72600 1.24400 C 3.05700 -2.71300 2.38100 C 2.33800 -2.11500 3.59200 C 1.27000 -1.15400 3.10000 C 2.15100 0.03200 2.68300 C 3.19600 0.07600 3.78800 O 3.93800 1.02100 3.98300 N 3.17400 -1.18300 4.31100 O 4.05400 -1.65700 5.28400 S 3.38300 -1.70500 6.79900 O 4.42700 -2.31500 7.61600 O 3.08700 -0.30900 7.10900 O 2.19100 -2.53900 6.62800 H 1.26500 1.98900 -0.55600 H 2.09600 2.17600 0.93800 H 3.82300 0.36100 1.36100 H 4.49300 -1.70100 1.15700 H 3.06500 -2.17300 0.29900 H 3.97500 -3.21900 2.70500 H 2.41300 -3.49600 1.96000 H 1.94500 -2.89800 4.24100 H 0.61200 -0.86000 3.92800 H 0.65100 -1.55100 2.29000 H 1.57300 0.96000 2.68200 end task opt xtb end Example: Geometry Optimization by for Organic Radical C\ :sub:`13`\ H\ :sub:`9` ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Perform geometry optimization by GFN2-xTB for an organic radical C\ :sub:`13`\ H\ :sub:`9`: .. code-block:: bash :linenos: :caption: xtb-4.inp xtb chrg 0 gfn 2 uhf 1 # The number of unpaired electrons is 1. end # C13H9 mol C 0. -1.2266 -2.135 C 0. 0.0000 -1.424 C 0. 1.2266 -2.135 C 0. -2.4574 -1.388 C 0. 0.0000 0.008 C 0. -1.2295 0.717 C 0. -2.4588 -0.032 C 0. -1.2128 2.117 H 0. -2.1632 2.672 C 0. 0.0000 2.807 C 0. 1.2128 2.117 C 0. 1.2295 0.717 C 0. 2.4588 -0.032 C 0. 2.4574 -1.388 H 0. 3.4035 -1.951 H 0. 3.4010 0.542 H 0. -3.4035 -1.951 H 0. -3.4010 0.542 H 0. 0.0000 3.908 H 0. 2.1632 2.672 H 0. -1.2130 -3.109 H 0. 1.2130 -3.109 end task opt xtb end