Tip

All input files can be downloaded: Files.

xpol

This option controls how to perform an XPol calculation.

Options 

method

Value	`mndo`
	`am1`
	`am1d`
	`rm1`
	`pm3`
	`pm3d`
	`pm6`
	`pmo`
	`pmow`
Default	`am1`

Define semi-empirical quantum chemistry method used for XPol calculation:

scf_type

Value	`r` for restricted Hartree-Fock
	`u` for unrestricted Hartree-Fock
Default	`u`

Define the SCF type for XPol calculation.

non_var: Use non-variational XPol calculation.

charge_type

Value	`mulliken` for Mulliken charges
	`dppc` for DPPC charges
Default	`mulliken`

Define the type of atomic charges used in XPol calculation.

print_level

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.

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:

xpol
    frag  0 1 1-3
    frag -1 1 4 5
end

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:

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:

\[H=\sum_{a=1}^N H_a^o+\frac{1}{2} \sum_{a=1}^N \sum_{b \neq a}^N H_{a b}(\rho_{b})\]

where effective interaction \(H_ab\) is:

\[H_{a b}\left(\rho_b\right)=-\sum_{i=1}^M V_i\left(\rho_b\right)+\sum_{A=1}^Q Z_A^a V_A\left(\rho_b\right)+E_{a b}^{\mathrm{XD}}\]

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:

\[E_{a b}^{\mathrm{XD}}\approx\sum_A^Q \sum_B^Q 4 \varepsilon_{A B}\left[\left(\frac{\sigma_{A B}}{R_{A B}}\right)^{12}-\left(\frac{\sigma_{A B}}{R_{A B}}\right)^6\right]\]

where \(\sigma_{ij} = \sqrt{sigma_i sigma_j}\) and \(\epsilon_{ij} = \sqrt{\epsilon_i \epsilon_j}\)

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:

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:

xpol

Options

Theoretical Background

Input Examples

Example: Geometry Optimization of a Water 32-mer Cluster

Options 

Theoretical Background 

Input Examples 

Example: Geometry Optimization of a Water 32-mer Cluster 