.. tip:: All input files can be downloaded: :download:`Files `. xpol ===== .. contents:: :local: This option controls how to perform an XPol calculation. Options ------------ .. option:: method .. list-table:: :stub-columns: 1 :widths: 5 20 * - Value - ``mndo`` * - - ``am1`` * - - ``am1d`` * - - ``rm1`` * - - ``pm3`` * - - ``pm3d`` * - - ``pm6`` * - - ``pmo`` * - - ``pmow`` * - Default - ``am1`` Define semi-empirical quantum chemistry method used for XPol calculation: .. option:: scf_type .. list-table:: :stub-columns: 1 :widths: 5 20 * - Value - ``r`` for restricted Hartree-Fock * - - ``u`` for unrestricted Hartree-Fock * - Default - ``u`` Define the SCF type for XPol calculation. .. option:: non_var .. list-table:: :stub-columns: 1 :widths: 5 20 Use non-variational XPol calculation. .. option:: charge_type .. list-table:: :stub-columns: 1 :widths: 5 20 * - Value - ``mulliken`` for Mulliken charges * - - ``dppc`` for DPPC charges * - Default - ``mulliken`` Define the type of atomic charges used in XPol calculation. .. option:: print_level .. list-table:: :stub-columns: 1 :widths: 5 20 * - Value - ``PrintDetails`` for verbose output. * - - ``PrintEssentials`` for standard output. * - - ``PrintNone`` for no output. * - Default - ``PrintEssentials`` for most cases. * - - ``PrintNone`` chosen when running MD simulations. The information printing level. .. option:: frag This defines fragments divide for system. The format is: - ``frag auto`` for automatic fragmentation by connectivity, in which each fragment is assumed as 0 charge and spin multiplicity is 1. - ``frag frag_charge frag_spin_multiplicity atom_range`` There can be arbitrary number of fragments, but all atoms must be included once and only once. Here is an example which defined two fragments, the first fragment has charge 0 and spin multiplicity 1, including atoms 1-3. And the second fragment has charge -1 and spin multiplicity 1, including atoms 4 and 5: .. code-block:: bash :linenos: xpol frag 0 1 1-3 frag -1 1 4 5 end .. option:: lj This defines Lennard-Jones parameters for non-bonded interactions between fragments. The format is: ``lj element sigma(kcal/mol) epsilon(angstrom)`` Here is an example which defined Lennard-Jones parameters for oxygen: .. code-block:: bash xpol lj O 3.24 0.16 end Lennard-Jones parameters **DO HAVE** a default value for each ``method``, which values will be shown in the output (with ``print_level`` being ``standard`` or ``verbose``). Users can set Lennard-Jones parameters to zero to turn off Lennard-Jones potential, but it is **NOT** recommended for most cases. Theoretical Background -------------------------------- XPol (Explicit Polarization) method is an fragment-based molecular orbital method for macromolecular systems or as a quantum force field for biomolecular and materials simulations. In which the effective Hamiltonian of the system is defined as sum of the Hamiltonian of each fragment and the interaction between fragments: .. math:: H=\sum_{a=1}^N H_a^o+\frac{1}{2} \sum_{a=1}^N \sum_{b \neq a}^N H_{a b}(\rho_{b}) where effective interaction :math:`H_ab` is: .. math:: H_{a b}\left(\rho_b\right)=-\sum_{i=1}^M V_i\left(\rho_b\right)+\sum_{A=1}^Q Z_A^a V_A\left(\rho_b\right)+E_{a b}^{\mathrm{XD}} The first and second terms are the electrostatic interaction between fragment a and b. The third term is rest part of the interaction, including exchange-repulsion and dispersion, which is approximated by Lennard-Jones potential in Qbics. In Lennard-Jones potential: .. math:: E_{a b}^{\mathrm{XD}}\approx\sum_A^Q \sum_B^Q 4 \varepsilon_{A B}\left[\left(\frac{\sigma_{A B}}{R_{A B}}\right)^{12}-\left(\frac{\sigma_{A B}}{R_{A B}}\right)^6\right] where :math:`\sigma_{ij} = \sqrt{sigma_i sigma_j}` and :math:`\epsilon_{ij} = \sqrt{\epsilon_i \epsilon_j}` Input Examples -------------------- Example: Geometry Optimization of a Water 32-mer Cluster ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ We perform an XPol(AM1) geometry optimization of a water 32-mer cluster. The input file is as follows: .. code-block:: bash :linenos: :caption: xpol-1.inp mol O 97.87475883 102.91148275 100.43222418 H 98.10048536 102.79050385 99.49670462 H 96.95991242 102.56796734 100.50737622 O 101.67212251 100.66547197 98.58765134 H 102.52651498 100.96781895 98.89553074 H 101.15843794 100.69592086 99.38268162 O 102.52639867 102.62956434 93.30170631 H 103.16438994 102.36526190 93.95819868 H 102.63407183 102.01335071 92.58047987 O 99.78963345 100.83849646 101.54069420 H 99.30912663 100.01645853 101.39552030 H 99.23940855 101.52167838 101.13381944 O 96.56328196 97.88535664 96.50308776 H 97.35092126 98.00792877 97.04885973 H 96.69651386 98.57745337 95.81794455 O 101.55651965 100.44188235 104.28664047 H 101.29231198 100.93029165 103.49525059 H 100.94211385 99.69552549 104.31716088 O 98.33903077 98.20095050 100.62403173 H 97.46688986 98.39143429 100.24987990 H 98.88724929 98.01898905 99.85319955 O 96.49085505 98.39266949 102.98073892 H 97.01839676 97.82501901 102.38352998 H 97.07914726 99.11997116 103.16170500 O 100.15845368 103.89054070 94.76042836 H 100.31025871 104.78666572 94.46770421 H 100.85419073 103.40624744 94.34461276 O 103.25183143 96.43746872 100.41332692 H 103.57397677 95.82213950 101.06596184 H 103.15126935 97.25278259 100.91227387 O 97.13798587 100.54608198 95.60727695 H 97.64529580 101.01421113 96.29426155 H 97.34490899 101.02744763 94.81552265 O 102.78775615 103.10597939 102.69170404 H 101.87495620 103.36745217 102.55724327 H 103.06489064 103.57474280 103.47719197 O 105.53095101 101.29716070 98.21079885 H 105.03215048 101.37688198 99.04530056 H 106.25038600 100.74038966 98.47794141 O 98.70268843 95.52690714 102.59502954 H 99.17322933 95.31157551 101.76029157 H 97.90610766 95.03528662 102.53533381 O 103.78641524 101.15992809 95.54113067 H 104.39936744 101.10524187 96.28116776 H 102.97842339 100.71623589 95.82585034 O 95.22662726 101.25576753 100.54757706 H 95.09181455 100.34655632 100.81400025 H 94.38907591 101.45434975 100.11156173 O 95.54973945 98.46833715 99.41156281 H 94.70879499 98.48021487 99.90099164 H 95.30623251 98.85282300 98.57362839 O 100.12536081 98.01698448 103.79646915 H 99.68330998 97.64271317 103.01896562 H 100.30026427 97.24458856 104.34618200 O 106.60609274 101.92504242 101.89716471 H 106.84368696 102.84494573 102.05245773 H 105.66648449 101.93410939 101.68417941 O 100.01126957 103.86673296 102.85030571 H 99.14512402 103.81766227 102.41019067 H 99.80965676 103.94951879 103.78709147 O 93.81511560 98.54368963 101.94850824 H 93.22139837 98.39098127 102.70887412 H 94.70212504 98.47257445 102.33070353 O 99.08033419 102.19637632 96.96666652 H 99.38148657 102.93806620 96.41226668 H 99.89727554 101.78103607 97.26624567 O 101.36021466 95.92993105 98.33435488 H 100.79388068 95.36142415 98.89251709 H 102.12231924 96.11773498 98.89898325 O 94.18044332 99.98166565 97.13799412 H 93.84436158 100.73600892 96.58620048 H 94.62724720 99.39243988 96.51265012 O 98.94940687 94.18348363 99.84354786 H 98.20879957 94.58885710 99.34924055 H 99.10203464 93.34846140 99.38941413 O 103.67742801 101.36877267 100.57996535 H 103.42785492 102.04841830 101.23853223 H 103.65884497 100.55268424 101.08486536 O 96.65886667 95.34817030 98.48343811 H 96.53805782 95.50558559 97.54435890 H 96.21487869 96.11049225 98.89898081 O 106.02135041 99.68723306 103.72962852 H 106.52031039 100.10392218 103.02914526 H 106.17171080 100.23799272 104.50209644 O 103.99051333 101.25322961 105.92784042 H 103.63808059 100.87479551 106.74301354 H 103.38222106 100.95049676 105.22335194 O 103.18696851 98.59196287 102.47424149 H 102.38198604 98.93354192 102.90584555 H 103.86566109 98.70048906 103.16468216 O 99.62185304 98.43979440 97.89631983 H 100.20109427 99.22329848 97.85712762 H 100.18480479 97.73316108 97.59075637 O 100.50489514 103.29505799 106.03644982 H 100.84890641 102.48413426 105.65062052 H 100.94370169 103.40392719 106.88536708 end xpol scf_type u charge_type dppc frag auto end task opt xpol end You can change ``am1`` to ``pm3``, ``pm6``, etc. to use other NDDO methods in XPol. The optimization trajectory is shown below: .. figure:: figs/xpol-1.gif