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In this section we simply provide a few examples of the QM/MM key block. In some examples, the MM_CONNECTION_TABLE and LINK_BONDS subkey blocks are not filled.
Example 3.1 - This example depicts a global optimization of the MM region with the simulated annealing-like optimizer available in the QM/MM program. The global search involves 100 ps of MD at 1000 K with 100 structures sampled in regular intervals during the simulation. Each of the 100 structures is then partially optimized, and then the 10 best are fully optimized. At the end of this, the lowest energy structure is used for the QM/MM run. Note that in this MD search, the QM atoms, including the link atoms are frozen.
QMMM
FORCE_FIELD_FILE sybyl.ff
OUTPUT_LEVEL 1
WARNING_LEVEL 1
ELSTAT_COUPLING_MODEL 1
OPTIMIZE
GLOBAL
METHOD MD_SEARCH
FREQUENCY ONCE
SUBEND
MD_SEARCH
TIME{PS} 100.0
N_STRUCTURES 100
TEMPERATURE 1000.0
SUBEND
SUBEND
MM_CONNECTION_TABLE
...
SUBEND
LINK_BONDS
...
SUBEND
END
Example 3.2 - In this example, custom charges are assigned to some of the atoms. Charges for atoms that were not given specific charges in the QMMM key block are assigned on a per atom-type basis from the force field file. Also note that this example has no LINK_BONDS subkey block. This is only allowed if there are not link bonds, as in the example in Figure 1-2a.
QMMM
FORCE_FIELD_FILE sybyl.ff
OUTPUT_LEVEL 1
WARNING_LEVEL 1
ELSTAT_COUPLING_MODEL 1
MM_CONNECTION_TABLE
...
SUBEND
CHARGES
0.4
0.3
3 -0.1
SUBEND