Features of this job:
Geometry optimization using ONIOM mechanical embedding.
MM region (water 1) described using OPLSAA.
QM region (water 2) described using PBE0/6-31G*.
$molecule input section contains user-defined MM bonds. A zero is used as a placeholder if there are no more connections.
Example 11.23 ONIOM optimization of water dimer.
$molecule 0 1 O -0.790909 1.149780 0.907453 186 2 3 0 0 H -1.628044 1.245320 1.376372 187 1 0 0 0 H -0.669346 1.913705 0.331002 187 1 0 0 0 O 1.178001 -0.686227 0.841306 186 5 6 0 0 H 0.870001 -1.337091 1.468215 187 4 0 0 0 H 0.472696 -0.008397 0.851892 187 4 0 0 0 $end $rem JOBTYPE opt METHOD pbe0 BASIS 6-31G* QM_MM_INTERFACE oniom FORCE_FIELD oplsaa USER_CONNECT true MOLDEN_FORMAT true $end $qm_atoms 4 5 6 $end
Features of this job:
Janus electronic embedding with a YinYang link atom (the glycosidic carbon at the C1 position of the deoxyribose).
MM region (deoxyribose) is described using AMBER99.
QM region (adenine) is described using HF/6-31G*.
The first 5 electronically excited states are computed with CIS. MM energy interactions between a QM atom and an MM atom (e.g., van der Waals interactions, as well as angles involving a single QM atom) are assumed to be the same in the excited states as in the ground state.
$molecule input section contains user-defined MM bonds.
Gaussian-blurred charges are used on all MM atoms, with a width set to 1.5 Å.
Example 11.24 Excited-state single-point QM/MM calculation on deoxyadenosine.
$molecule 0 1 O 0.000000 0.000000 0.000000 1244 2 9 0 0 C 0.000000 0.000000 1.440000 1118 1 3 10 11 C 1.427423 0.000000 1.962363 1121 2 4 6 12 O 1.924453 -1.372676 1.980293 1123 3 5 0 0 C 2.866758 -1.556753 0.934073 1124 4 7 13 18 C 2.435730 0.816736 1.151710 1126 3 7 8 14 C 2.832568 -0.159062 0.042099 1128 5 6 15 16 O 3.554295 1.211441 1.932365 1249 6 17 0 0 H -0.918053 0.000000 -0.280677 1245 1 0 0 0 H -0.520597 -0.885828 1.803849 1119 2 0 0 0 H -0.520597 0.885828 1.803849 1120 2 0 0 0 H 1.435560 0.337148 2.998879 1122 3 0 0 0 H 3.838325 -1.808062 1.359516 1125 5 0 0 0 H 1.936098 1.681209 0.714498 1127 6 0 0 0 H 2.031585 -0.217259 -0.694882 1129 7 0 0 0 H 3.838626 0.075227 -0.305832 1130 7 0 0 0 H 4.214443 1.727289 1.463640 1250 8 0 0 0 N 2.474231 -2.760890 0.168322 1132 5 19 27 0 C 1.538394 -2.869204 -0.826353 1136 18 20 28 0 N 1.421481 -4.070993 -1.308051 1135 19 21 0 0 C 2.344666 -4.815233 -0.582836 1134 20 22 27 0 C 2.704630 -6.167666 -0.619591 1140 21 23 24 0 N 2.152150 -7.057611 -1.455273 1142 22 29 30 0 N 3.660941 -6.579606 0.239638 1139 22 25 0 0 C 4.205243 -5.691308 1.066416 1138 24 26 31 0 N 3.949915 -4.402308 1.191662 1137 25 27 0 0 C 2.991769 -4.014545 0.323275 1133 18 21 26 0 H 0.951862 -2.033257 -1.177884 1145 19 0 0 0 H 2.449361 -8.012246 -1.436882 1143 23 0 0 0 H 1.442640 -6.767115 -2.097307 1144 23 0 0 0 H 4.963977 -6.079842 1.729564 1141 25 0 0 0 $end $rem METHOD cis BASIS 6-31G* QM_MM_INTERFACE janus USER_CONNECT true FORCE_FIELD amber99 GAUSSIAN_BLUR true GAUSS_BLUR_WIDTH 15000 CIS_N_ROOTS 5 CIS_TRIPLETS false MOLDEN_FORMAT true PRINT_ORBITALS true $end $qm_atoms 18 19 20 21 22 23 24 25 26 27 28 29 30 31 $end
Features of this job:
An MM-only calculation. BASIS and EXCHANGE need to be defined, in order to prevent a crash, but no electronic structure calculation is actually performed.
All atom types and MM interactions are defined in $force_field_params using the CHARMM27 force field. Atomic charges, equilibrium bond distances, and equilibrium angles have been extracted from a HF/6-31G* calculation, but the force constants and van der Waals parameters are fictitious values invented for this example.
Molecular dynamics is propagated for 10 steps within a microcanonical ensemble (NVE), which is the only ensemble available at present. Initial velocities are sampled from a Boltzmann distribution at 400 K.
Example 11.25 MM molecular dynamics with user-defined MM parameters.
$molecule -2 1 C 0.803090 0.000000 0.000000 -1 2 3 6 0 C -0.803090 0.000000 0.000000 -1 1 4 5 0 H 1.386121 0.930755 0.000000 -2 1 0 0 0 H -1.386121 -0.930755 0.000000 -2 2 0 0 0 H -1.386121 0.930755 0.000000 -2 2 0 0 0 H 1.386121 -0.930755 0.000000 -2 1 0 0 0 $end $rem METHOD hf BASIS sto-3g QM_MM_INTERFACE MM FORCE_FIELD charmm27 USER_CONNECT true JOBTYPE aimd TIME_STEP 42 AIMD_STEPS 10 AIMD_INIT_VELOC thermal AIMD_TEMP 400 $end $force_field_params NumAtomTypes 2 AtomType -1 -0.687157 2.0000 0.1100 AtomType -2 -0.156422 1.3200 0.0220 Bond -1 -1 250.00 1.606180 Bond -1 -2 300.00 1.098286 Angle -2 -1 -2 50.00 115.870 Angle -2 -1 -1 80.00 122.065 Torsion -2 -1 -1 -2 2.500 180.0 2 $end
Further examples of QM/MM calculations can be found in the $QC/samples directory, including a QM/MM/PCM example, pcm_qmmm_crambin.in. This calculation consists of a protein molecule (crambin) described using a force field, but with one tyrosine side chain described using electronic structure theory. The entire QM/MM system is placed within an implicit solvent model, of the sort described in Section 11.2.3.