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(June 30, 2021)

A QM/MM job is requested by setting the *$rem* variables QM_MM_INTERFACE
and FORCE_FIELD.
Also required are a *$qm_atoms* input section and appropriate modifications to the *$molecule*
section, as described above. Additional job control variables are detailed here.

QM_MM_INTERFACE

Enables internal QM/MM calculations.

TYPE:

STRING

DEFAULT:

NONE

OPTIONS:

MM
Molecular mechanics calculation (*i.e.*, no QM region)
ONIOM
QM/MM calculation using two-layer mechanical embedding
JANUS
QM/MM calculation using electronic embedding

RECOMMENDATION:

The ONIOM model and Janus models are described above. Choosing MM
leads to no electronic structure calculation. However, when using MM, one
still needs to define the *$rem* variables BASIS and EXCHANGE
in order for Q-Chem to proceed smoothly.

FORCE_FIELD

Specifies the force field for MM energies in QM/MM calculations.

TYPE:

STRING

DEFAULT:

NONE

OPTIONS:

AMBER99
AMBER99 force field
CHARMM27
CHARMM27 force field
OPLSAA
OPLSAA force field

RECOMMENDATION:

None.

CHARGE_CHARGE_REPULSION

The repulsive Coulomb interaction parameter for YinYang atoms.

TYPE:

INTEGER

DEFAULT:

550

OPTIONS:

$n$
Use Q = $n\times {10}^{-3}$

RECOMMENDATION:

The repulsive Coulomb potential maintains bond lengths involving YinYang
atoms with the potential $V(r)=Q/r$. The default is parameterized for carbon atoms.

GAUSSIAN_BLUR

Enables the use of Gaussian-delocalized external charges in a QM/MM calculation.

TYPE:

LOGICAL

DEFAULT:

FALSE

OPTIONS:

TRUE
Delocalizes external charges with Gaussian functions.
FALSE
Point charges

RECOMMENDATION:

None

GAUSS_BLUR_WIDTH

Delocalization width for external MM Gaussian charges in a Janus calculations.

TYPE:

INTEGER

DEFAULT:

NONE

OPTIONS:

$n$
Use a width of $n\times {10}^{-4}$ Å.

RECOMMENDATION:

Blur all MM external charges in a QM/MM calculation with the specified width.
Gaussian blurring is currently incompatible with PCM calculations. Values of
1.0–2.0 Å are recommended in Ref. 243.

MODEL_SYSTEM_CHARGE

Specifies the QM subsystem charge if different from the *$molecule* section.

TYPE:

INTEGER

DEFAULT:

NONE

OPTIONS:

$n$
The charge of the QM subsystem.

RECOMMENDATION:

This option only needs to be used if the QM subsystem (model system)
has a charge that is different from the total system charge.

MODEL_SYSTEM_MULT

Specifies the QM subsystem multiplicity if different from the *$molecule* section.

TYPE:

INTEGER

DEFAULT:

NONE

OPTIONS:

$n$
The multiplicity of the QM subsystem.

RECOMMENDATION:

This option only needs to be used if the QM subsystem (model system)
has a multiplicity that is different from the total system multiplicity.
ONIOM calculations must be closed shell.

USER_CONNECT

Enables explicitly defined bonds.

TYPE:

STRING

DEFAULT:

FALSE

OPTIONS:

TRUE
Bond connectivity is read from the *$molecule* section
FALSE
Bond connectivity is determined by atom proximity

RECOMMENDATION:

Set to TRUE if bond connectivity is known, in which case this connectivity must be
specified in the *$molecule* section. This greatly accelerates MM calculations.

MM_SUBTRACTIVE

Specifies whether a subtractive scheme is used in the ${E}_{\mathrm{Coul}}$, Eq. (11.51), portion of the calculation.

TYPE:

LOGICAL

DEFAULT:

FALSE

OPTIONS:

FALSE
Only pairs that are not 1-2, 1-3, or 1-4 pairs are used.
TRUE
All pairs are calculated, and then the pairs that are double counted (1-2, 1-3, and 1-4) are subtracted out.

RECOMMENDATION:

When running QM/MM or MM calculations there is not recommendation. When running a QM/MM-Ewald calculation
the value must be set to TRUE.