Custer QM/MM model for a zeolite system
The first file, zeolite_cluster.chm starts from a the crystal structure of the zeolite zsm-5 and generates a spherical cluster from it. As an intermediate step, the unit cell of the zeolite is output as fragment object zsm5.c. You can visualise this with Aten and pick which of the atoms you want to centre the cluster on. The cluster is actually created by the following ChemShell command:
construct_cluster \
coords=zsm5.c \
crystal_type=covalent \
radius_cluster=25.0 \
radius_active=10.0 \
origin_atom=5 \
bq_density=2 \
bq_margin=5.0 \
cluster=zsm5.clus \
mm_theory=dl_poly : mm_defs=zeolite.ff
This cluster cutting procedure will use the atom type assignments and associated charges as specified on the mm_theory argument.
The atoms in the resulting cluster are ordered outwards from the centre, so that atom 1 is the atom that was specified as the origin. There is a Tcl loop in the input file that checks this is the case.
Once the cluster has been generated, a short QM/MM calculation is performed with it, specifying as the QM atom a single Si atom (atom 1, the central atom) , which will be H-terminated to give an SiH4 group embedded in the zeolite framework.
The basis set used is that stored internally to ChemShell using the dzp keyword.
energy coords=zsm5.clus energy=e \
theory=hybrid : [ list coupling=shift \
dipole_adjust=yes \
mm_theory=dl_poly : { mm_defs= zeolite.ff} \
qm_theory=gamess : basisspec = { { dzp * } } qm_region= $hit ]
The dipole_adjust=yes flag is used in the QM/MM calculation to make a bond dipole correction to the charges of the first layer of MM atoms. This is a special adjustment for silicate materials using Si/O charges of 1.2/-0.6 (see the hybrid section of the manual).
As an example of a slightly more complex QM/MM calculation, in which the structure of an adsorbate has been added, see the file zeo_nh4.chm.
If interested, you can build your own clusters including additional atoms using the following procedure.
- The cluster can be loaded into ccp1gui and a substrate edited into the active site, using the "Editing Tools" option.
- If preferred, some or all of the newly added atoms can be represented as z-matrix atoms. This way optimisation can proceed in internal coordinates, and the coordinates can be edited to produce good starting geometries.
- If it is intended to work in z-matrix coordinates, is necessary to add
three dummy atoms to the top of the file to ensure that the coordinates obey standard z-matrix
conventions:
coordinates angstrom X 0.000000 0.000000 0.000000 X 0.000000 0.000000 1.000000 X 1.000000 0.000000 0.000000 si -11.565108 1.124293 -4.496420 .....This can be done using the "Insert Atom" option of the coordinate editor window. - The result of this editing operation can be saved from within the zmatrix editor using the File menu.
- The resulting mixed internal/cartesian Z-matrix can be loaded and used as the starting point for a geometry optimisation, as shown in zeol_nh4.chm.
In order to run this example you need GAMESS-UK (specifically the rungamess script) in your path, and you need the following files from the zeol1_cff directory: zeolite_cluster.chm, zeolite.ff, zeo_nh4.chm, and zeo_nh4.zmt.