Example Input

Let Figure 2-1 show the molecular system that we want to simulate and the intended partitioning. Note that this is the same system as shown in Figure 1-1 except that a non-bonded water molecule has been added to the MM region.

Figure 2-1. Sample structure. Atom numberings and the QM/MM atom types (QM, MM and LI) are shown.

Example 2.1 below shows the ADF input file for the simulation with the geometry defined in Cartesian coordinates. The initial atomic coordinates of the full QM/MM system are defined as they would be in a normal ADF run with the ATOMS and GEOVAR key blocks. Notice that the subkey blocks within the QMMM key block (e.g. MM_CONNECTION_TABLE) end with SUBEND. If they were closed by 'END' ADF would consider the QMMM key block complete at that point.

Example 2.1:

Title example QM/MM input
Fragments
 C C.t21
 H H.t21
 O O.t21
End

Symmetry NOSYM
Charge 0 0

ATOMS
 1 C 0.00000 0.00000 0.00000
 2 O 1.48700 0.00000 0.00000
 3 C -0.76430 1.32381 0.00000
 4 C -0.76428 -1.32378 -0.00002
 5 H -0.50028 -1.89680 -0.89230
 6 H -0.50028 -1.89683 0.89224
 7 H -1.83868 -1.12409 -0.00002
 8 H -1.40364 1.39261 -0.88358
 9 H -1.40364 1.39261 0.88358
 10 C 0.22461 2.48208 0.00000
 11 H 0.85235 2.42365 -0.89260
 12 H 0.85235 2.42365 0.89260
 13 C -0.53689 3.80103 0.00000
 14 H -1.16478 3.85787 -0.89260
 15 H -1.16478 3.85787 0.89260
 16 C 0.45222 4.95913 -0.00000
 17 H 1.08538 4.90988 -0.88932
 18 H 1.08538 4.90988 0.88932
 19 H -0.08590 5.91026 0.00000
 20 H 2.43700 1.64545 0.00000
 21 O 3.03926 2.50556 -0.00000
 22 H 3.96191 2.28678 -0.45094
END


QMMM
 FORCE_FIELD_FILE sybyl.ff
 RESTART_FILE mm.restart
 OUTPUT_LEVEL=1
 WARNING_LEVEL=1
 ELSTAT_COUPLING_MODEL=0
 LINK_BONDS
 1 - 3 1.38000 H
 SUBEND

 MM_CONNECTION_TABLE
 1 C_2 QM 2 3 4
 2 O_2 QM 1
 3 C_3 LI 1 8 9 10
 4 C_3 QM 1 5 6 7
 5 H QM 4
 6 H QM 4
 7 H QM 4
 8 H MM 3
 9 H MM 3
 10 C_3 MM 3 11 12 13
 11 H MM 10 
 12 H MM 10
 13 C_3 MM 10 14 15 16
 14 H MM 13 
 15 H MM 13
 16 C_3 MM 13 17 18 19
 17 H MM 16 
 18 H MM 16
 19 H MM 16 
 20 H MM 21
 21 O_3 MM 20 22
 22 H MM 21
 SUBEND
END


GEOMETRY
 ITERATIONS 20
 CONVERGE E=1.0E-3 GRAD=0.0005
 STEP RAD=0.3 ANGLE=5.0
 DIIS N=5 OK=0.1 CYC=3
END

XC
 LDA VWN
 GGA POSTSCF Becke Perdew
End

Integration 3.0

SCF
 Iterations 60
 Converge 1.0E-06 1.0E-6
 Mixing 0.20
End
End Input