The basic idea behind a hybrid QM/MM simulation in NAMD is to use a classical force field to treat the classical atoms in the system (or ``MM atoms"), and pass the information that describes the quantum atoms in the system (or ``QM atoms") to a Quantum Chemistry (QC) software, which is expected to produce gradients for all QM atoms, as well as the total energy of the QM region (and optionally partial charges). All bonded and non-bonded interactions among MM atoms are handled by NAMD's force field. Similarly, all bonded and non-bonded interactions among QM atoms are handled by the QC software in its chosen theory level. Treatment of covalent bonds between QM and MM atoms will be described in a following section.
The non-bonded interactions between QM and MM atoms are handled differently, and can be modified and regulated by the user. Van der Waals interactions are always calculated, and can be done using either the default force field parameters, or specific (user-defined) parameters for QM atoms. Parameter modifications for QM atoms have been proposed in order to compensate for over-polarization that these atoms may exhibit in hybrid QM/MM simulations. Larger van der Waals radii and/or shallower well depths should then be provided for all element types that occur among QM atoms (see the ``qmVdwParams" keyword).