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 results29.1.
The QM/MM module in NWChem is driven by the molecular dynamics module. This module currently works for any QM method that has analytic gradients29.2. The input for this requires the definition of chemical system via the same interface that is used by the MD module (c.f. Section 27). 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 geometry29.3. 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.
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 no default for this and the input must be present for a QM/MM simulation.
All other parameters that control the QM/MM simulation are set via the input to nwmd (see chapter 27).