Molecular mechanics calculation¶

If you have not already done so, you should take a look at the eT_launch page to get an understanding of how the launch script works.

Setting up a QM/MM calculation¶

A QM/MM calculation can be performed with a HF or CC wave function. The available MM methods are polarizable QM/fluctuating charges and electrostatic embedding. To perform a QM/MM calculation it is necessary to include all the sections for the corresponding HF or CC calculation and to include the molecular mechanics and specify the forcefield keyword as non-polarizable (default) or fq. Notice that parameters the force fields must be included in the geometry section. E.g. we write

- molecular mechanics
  forcefield: fq

In the geometry section, the QM and MM portions have to be separated by a line containing --. You have to specify the N-th MM fragment with the label [IMol = N] after the atomic symbol. The FQ force field requires so specify for each atom the electronegativity chi and the chemical hardness eta, while for the electrostatic embedding the charge of each MM atom needs to be specified. The parameters need to be set after the XYZ coordinates, for instance for a FQ forcefield:

- geometry
  basis: cc-pVDZ
  O          0.009319    1.133156    0.000000
  H          0.023452    0.185621    0.000000
  H          0.906315    1.422088    0.000000
  --
  O [IMol=   1]         -0.042964   -1.404707   -0.000000      [chi=0.68539204573,eta=0.3666239485]
  H [IMol=   1]         -0.419020   -1.818953    0.760190      [chi=0.49933907696,eta=0.8243062837]
  H [IMol=   1]         -0.419020   -1.818953   -0.760190      [chi=0.49933907696,eta=0.8243062837]

A minimal working example for an electrostatic embedding is:

- do
  ground state

- molecular mechanics
  forcefield: non-polarizable

- method
  hf

- geometry
  basis: cc-pVDZ
  H          0.023452    0.185621    0.000000
  H          0.906315    1.422088    0.000000
  O          0.009319    1.133156    0.000000
  --
  O [Mol=   1]         -0.042964   -1.404707   -0.000000     [q=-0.834]
  H [Mol=   1]         -0.419020   -1.818953    0.760190     [q=+0.417]
  H [Mol=   1]         -0.419020   -1.818953   -0.760190     [q=+0.417]

At the end of the output file you can find the computed energy as well as the summary of QM/MM energetics

- Summary of RHF wave function energetics (a.u.):

   HOMO-LUMO gap:                  0.684637098457
   Nuclear repulsion energy:       9.307879526626
   Electronic energy:            -85.682927748575
   Total energy:                 -76.375048221949

- Summary of QM/MM energetics:
                                       a.u.             eV     kcal/mol
   QM/MM SCF Contribution:         0.324293061350     8.82446   203.497
   QM/MM Electrostatic Energy:    -0.349605908858    -9.51326  -219.381