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# 33. Combined quantum and molecular mechanics

Combined or hybrid Quantum Mechanics and Molecular Mechanics (QM/MM) is a simulation methodology that is about 15 years old but in all the literature there are cautions that calibration computations must be done to validate the model for each particular chemical system studied. This is not a black box style computation and the NWChem users are advised that without calibration QM/MM may not give the appropriate results33.1.

The QM/MM module in NWChem is driven by the molecular dynamics module. This module currently works for any QM method that has analytic gradients33.2. The input for this requires the definition of chemical system via the same interface that is used by the MD module (c.f. Section 31). The extensions to this interface include the definition of ``Quantum'' atoms and ``Link'' where appropriate. The QM information must be present in the traditional NWChem input deck except for the geometry33.3. The geometrical information will be constructed automatically by nwmd. For dynamics and free energy simulations the input is again identical to that for nwmd with limitations on the kinds of simulations that can be done. Link atoms are defined by the molecular dynamics module, based on the specification of the quantum atoms in the prepare module. For the link atoms, basis sets `X_L` need to be defined in the basis set input block.

The QM/MM module is invoked with the task directive where the ``theory'' is QMMM. The recognized operations on the QM/MM theory directive are energy, optimize, and dynamics.

      task qmmm (energy | optimize | dynamics)

Tasks `gradient`, `saddle`, `frequencies` and `thermodynamics` are currently not available in the QM/MM mode.

The QM/MM input consists of the standard NWChem input block:

      qmmm
        ...
      end

The `qmmm` has the following the additional sub-directive that the user may specify for the particular simulation. These options currently are:

-     eatoms < real eatoms>

  There is one compound input directive that must exist for the QM/MM simulation to proceed. This sets the relative zero of energy for the QM component of the system. It is not incorrect to leave this value as zero but the energetics of the QM system will likely over shadow the MM component of the system. Properties based on energy fluctuations of the system will be overly sensitive to the energy of the QM component of the system. The zero of energy for the MM system is by definition of most parameterized force fields the separated atom energy. The zero of energy for QM systems by definition of most QM methods is the vacuum. The a priori determination of the separated atom energy for a particular QM method is not well defined and thus leads to a number of assumptions or guess work depending upon the particular QM method being utilized. Therefor, the determination of the QM separated atom energy (``eatoms'') is left to the user. There is no default for this and the input must be present for a QM/MM simulation.

-     qatoms < real qatoms>

  This input directive is used to specify the total charge on the set of quantum atoms.

-     link hydrogen

  This directive specified to use hydrogens as link atoms. The default is to use the next group VII atom.

-     nobq ( hydrogen | all | none )

  This directive specifies that hydrogen atoms, all atoms, or no atoms, respectively, bonded to link atoms will carry a zero charge in the QM part of the calculation.

All other parameters that control the QM/MM simulation are set via the input to nwmd (see chapter 31).

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