Training nequip on pdb datasets

[shreshthtuli]

Hi. I am wondering if it is possible to train and test nequip on pdb datasets with pairs of molecules, such as https://data.sbgrid.org/dataset/684/. Any help is greatly appreciated :)

[Linux-cpp-lisp]

Hi @shreshthtuli ,

Thanks for your interest in our code!

We generally recommend converting all data into the extXYZ format, which can be easily done by constructing ASE Atoms objects somehow (https://wiki.fysik.dtu.dk/ase/ase/atoms.html) and writing them to an XYZ file with ase.io.write. I'm not familiar with the dataset you've linked, but in general just remember that in the default setup MLIPs like Allegro learn a mapping between a specific geometry and an energy, so if that sounds applicable then you should be fine to go ahead with the default setup.