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<H1><A NAME="SECTION003500000000000000000">
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33. Combined quantum and molecular mechanics</A>
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</H1>
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<P>
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<A NAME="sec:qmmm"></A>
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<P>
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Combined or hybrid Quantum Mechanics and Molecular Mechanics (QM/MM)
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is a simulation methodology that is about 15 years old but in all the
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literature there are cautions that calibration computations must be
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done to validate the model for each particular chemical system
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studied. This is not a black box style computation and the NWChem
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users are advised that without calibration QM/MM may not give the
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appropriate results<A NAME="tex2html75"
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HREF="footnode.html#foot9533"><SUP>33.1</SUP></A>.
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<P>
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The QM/MM module in NWChem is driven by the molecular dynamics module.
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This module currently works for any QM method that has
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analytic gradients<A NAME="tex2html76"
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HREF="footnode.html#foot9512"><SUP>33.2</SUP></A>. The input
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for this requires the definition of chemical system via the same
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interface that is used by the MD module (c.f. Section
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<A HREF="node33.html#sec:nwmd">31</A>). The extensions to this interface include the
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definition of ``Quantum'' atoms and ``Link'' where appropriate. The
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QM information must be present in the traditional NWChem input deck
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except for the geometry<A NAME="tex2html77"
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HREF="footnode.html#foot9514"><SUP>33.3</SUP></A>. The geometrical information will
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be constructed automatically by nwmd. For dynamics and free energy
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simulations the input is again identical to that for nwmd with
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limitations on the kinds of simulations that can be done.
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Link atoms are defined by the molecular dynamics module, based on
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the specification of the quantum atoms in the prepare module. For
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the link atoms, basis sets <code>X_L</code> need to be defined in the
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basis set input block.
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<P>
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The QM/MM module is invoked with the task directive where the
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``theory'' is QMMM. The recognized operations on the QM/MM theory
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directive are energy, optimize, and dynamics.
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<P>
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<PRE>
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task qmmm (energy | optimize | dynamics)
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</PRE>
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<P>
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Tasks <code>gradient</code>, <code>saddle</code>, <code>frequencies</code> and
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<code>thermodynamics</code> are currently not available in the QM/MM mode.
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<P>
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The QM/MM input consists of the standard NWChem input block:
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<PRE>
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qmmm
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...
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end
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</PRE>
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<P>
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The <code>qmmm</code> has the following the additional sub-directive that the user
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may specify for the particular simulation. These options currently are:
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<P>
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<UL>
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<LI><PRE>
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eatoms < real eatoms>
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</PRE>
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<P>
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There is one compound input directive that must exist for the QM/MM
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simulation to proceed. This sets the relative zero of energy for the
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QM component of the system. It is not incorrect to leave this value as
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zero but the energetics of the QM system will likely over shadow the
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MM component of the system. Properties based on energy fluctuations
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of the system will be overly sensitive to the energy of the QM
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component of the system. The zero of energy for the MM system is by
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definition of most parameterized force fields the separated atom
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energy. The zero of energy for QM systems by definition of most QM
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methods is the vacuum. The <I>a priori</I> determination of the
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separated atom energy for a particular QM method is not well defined
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and thus leads to a number of assumptions or guess work depending upon
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the particular QM method being utilized. Therefor, the determination
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of the QM separated atom energy (``eatoms'') is left to the user.
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There is no default for this and the input <B>must</B> be present for a
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QM/MM simulation.
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<P>
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</LI>
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<LI><PRE>
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qatoms < real qatoms>
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</PRE>
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<P>
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This input directive is used to specify the total charge on the set
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of quantum atoms.
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<P>
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</LI>
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<LI><PRE>
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link hydrogen
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</PRE>
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<P>
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This directive specified to use hydrogens as link atoms. The default
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is to use the next group VII atom.
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<P>
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</LI>
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<LI><PRE>
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nobq ( hydrogen | all | none )
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</PRE>
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<P>
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This directive specifies that hydrogen atoms, all atoms, or no atoms,
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respectively, bonded to link atoms will carry a zero charge in the
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QM part of the calculation.
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<P>
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</LI>
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</UL>
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All other parameters that control the QM/MM simulation are set via the
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input to nwmd (see chapter <A HREF="node33.html#sec:nwmd">31</A>).
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<P>
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<ADDRESS>
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Edoardo Apra
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2004-05-25
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