QM/MM with polarizable force fields
***********************************

ADF DFT QM/MM DRF QM/FQ UV/Vis Excitations

This (technical) example shows how to make an input for the QM/MM
methods DRF and QM/FQ in which both polarizable force fields are used.

You can study chemistry in solution, as contrasted to the gas phase,
with the implementation of implicit solvation models (continuum
solvation) like COSMO and SM12, or explicit solvation models like
molecular dynamics or multi-level methods. Many multi-level methods
exist that can treat solvation effects, like QM/MM with mechanical or
electrostatic embedding, QM/MM with polarizable force-fields like DRF
and QM/FQ, or frozen density embedding (FDE). Using implicit solvation
models is relatively straightforward. For explicit solvation models
using multi-level methods, like DRF and QM/FQ you will need to define
regions.

The geometry for such QM/MM calculations could be taken from snapshots
of a molecular dynamics calculation.


DRF
===

To demonstrate how to set up a DIM/QM DRF (Discrete Solvent Reaction
Field) calculation using AMSinput, we will use water in water as an
example. DRF is a QM/MM method in which the MM atoms interact with the
QM region via induced dipoles and static charges. DRF facilitates
calculating the optical properties of molecules. One should use the
'Single Point' Task.

   Download the following xyz file: file "water_in_water.xyz"
   Open AMSinput: **File → Import Coordinates...** and select 'water_in_water.xyz'
   Select Task **Single Point**
   Select XC functional **Model:SAOP**
   Select Basis set **TZ2P** and Core **None**
   Select Numerical Quality **Good**
   Use the panel bar **Properties → Excitations (UV/Vis), CD** command
   For the 'Type of excitations' option, Select 'SingletOnly'
   Select the middle water molecule
   (for example with **Model → Coordinates** and select the first 3 atoms)
   Use the panel bar **Model → Regions** command
   click the [image: AddButton][image] button next to Regions, and rename Region_1 to "Solute"
   Select all other atoms of the complex (by Select → Invert Selection)
   click the [image: AddButton][image] button again, and rename Region_2 to "Solvent"
   Use the panel bar **Model → DIM/QM** command
   For the 'Method' option, Select 'DRF'
   Click the check button 'QM part' for the 'Solute' region
   Click the check button 'DIM part' for the 'Solvent' region

In the next step atomic charges for the DRF region are computed using
MDC-Q charges (LDA functional, DZP basis set). The atomic
polarizabilities are taken from a inner database including fitted
parameters for the H, C, N, O, F, S, Cl, Br, and I atoms, and non-
optimized parameters for most other atoms.

   For the 'Charges' option, Select 'MDC-Q'
   Save as 'Water_DRF'
   **File → Run**
 [image]


QM/FQ(Fμ)
=========

To demonstrate how to set up a QM/FQ (Quantum Mechanics/Fluctuating
Charges) or QM/FQFμ (if Fluctuating Dipoles are included) calculation
using AMSinput, we will use 2-methyloxirane in water as an example.
These are QM/MM methods in which the MM atoms interact with the QM
region via induced charges and possibly dipoles. The MM charges and
dipoles are determined self-consistently along with the ground-state
QM density. QM/FQ(Fμ) also facilitates calculating the optical
properties of molecules. Since the charges and dipoles depend on the
QM density, explicit terms also appear within response equations that
are solved to simulate spectroscopic and excited-state properties of
the QM system.

One should use the 'Single Point' Task.

   Download the following xyz file: file "methyloxirane_in_water.xyz"
   Open AMSinput: **File → Import Coordinates...** and select 'methyloxirane_in_water.xyz'
   Select Task **Single Point**
   Select XC functional **GGA:PBE**
   Select Basis set **TZP** and Core **None**
   Select Numerical Quality **Good**
   Use the panel bar **Properties → Excitations (UV/Vis), CD** command
   For the 'Type of excitations' option, Select 'SingletOnly'
   Select the 2-methyloxirane molecule
   (for example by clicking a carbon atom then Select → Select Molecule)
   Use the panel bar **Model → Regions** command
   click the [image: AddButton][image] button next to Regions, and rename Region_1 to "Solute"
   Select all other atoms of the complex (by Select → Invert Selection)
   click the [image: AddButton][image] button again, and rename Region_2 to "Solvent"
   Click on the right arrow at the end of the 'Solvent' line
   Use the 'Hidden' command from the menu that appears
 [image]

Hidden here means that the molecules in the 'Solvent' region are
hidden. The 'Solvent' region is still visible because it is colored.

The GUI has parameters for QM/FQ in case water is the solvent in the
FQ region.

   Use the panel bar **Model → QM/FQ** command
   Check the Enable check button
   Click the check button 'QM part' for the 'Solute' region
   Click the check button 'FQ part' for the 'Solvent' region
   Save as 'methyloxirane_QMFQ'
   **File → Run**
 [image]
