RDKit Optimize Geometry

In this node, what are the units of the energy column?  Is there any way can I calculate the difference between the energy of the input conformer and the minimized structure?



Hi Alastair,

the energy unit of all force fields offered in the RDKit Optimize Geometry is kcal/mol.

There was no way until today to calculate the difference between the energy of the input conformer and the minimized structure. I had to make a change for this, which I just checked in - it will be available in the next nightly community build. You can now set as Advanced parameter an iterations value of 0, which will turn of the optimization completely and will just calculate the energy for the input conformers. That way you can have two of the RDKit Optimizing Geometry nodes in a row, one for the input energy calculation, the other one for the opimization and its energy calculation. And with a third node in that row you can easily calculate the difference between the two energy columns, e.g. with a Java Snippet node.

Hope this helps!

Kind regards,

Manuel Schwarze

Thanks Manuel - very helpful indeed!


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