I'm trying to design a calculator for use with ASE (Atomic Simulation
Environment: https://wiki.fysik.dtu.dk/ase/) which uses openbabel to get
energies using UFF and ghemical (for now). For this, I have a couple of
Is it possible to automatically add bonds. In our code, we do not
represent bonds as we usually just perform DFT calculations. I know that
avogadro/openbabel adds bonds automatically when reading an .xyz file
with openbable, so this should be possible.
When I set up the force field, I can get the energy with FF.Energy(). Is
it possible to get the gradient with respect to nuclear/atomic
coordinates. Something like this must be available for use in
openbabels internal structure optimizers. I can see OBForceField has a
protected method GetGradient. Does this give me that, and how do I
access it from python?
For the record: I need the forces to perform some specialized
optimizations, such as the Nudge Elastic Band method.