Fortran Format

Internal cordinates found in QM programs,in order to cancel 6 degrees of freedom.

We start numerating atoms. Eg. Benzene, 12 atoms, 6 C, 6 H. We establish our first atom as a reference
(internal coordinates). Having defined our reference next atoms are placed regarding our firs atom. The
same for angles and dyhedral angles. The three first carbons do not need to specify DI, because 3 points
always are on the same plane. However, counting form the fourth carbon we must specify a DI (even if
it is 0).

Torsion angles can be modeled by a quantum approach, but is such a difficult task modeling them by a
classical approach.
Tiles,

QM-MM: Van der Waals interaction, Electronic energy due to the external region, Energy due to the
bonds

QM/MM: External we have punctual charges, but internally we only have electron density.

Open Babel: translate formats from Z-matrix to .xyz and visualize using Jmol.

Build the code with VI

vi h20.zmat

1O
2H
3H

#
comment

01
O
H 1 1.0
H 1 1.0 2 108.0

save :x!
babel -L format

babel -igzmat h2o.zmat -oxyz h2o.xyz

vi h2o.xyz