I am using both versions 1.20 and 1.99.0 on my MacOS, and I found that these two versions do geometry optimization differently. What I was doing is to optimize the structures of several molecules connected with hydrogen bonds. When using v1.20, the work was done slowly, but the final structure looks quite good. The v1.99.0 performed the optimization (MMFF94, convergence 1E-7, step limits: 100000)very fast, but the final structure is not as good as that done by v1.20. It seems that the the work has not been completely done when using v1.99.0 (I repeated the optimization for many times). I see there are options in v1.99.0 to tune the parameter for hydrogen bonds, but I am not sure how different it is to that in v1.20.
What do you see from the difference?
Just to clarify, how are you doing the optimization in 1.99? Via the Open Babel ⇒ Optimize Geometry or via the Extensions menu?
If you have a file or two to share, I’d appreciate it. The newer optimization framework almost certainly still has bugs.
I used the one via the Open Babel. The one under the “Extension” menu does not work on my MacOS (apple M3 chip).
Here are two structures after optimization. The first one is done using v1.20, and the second is done using v1.99.0. Please pay attention to the hydrogen bonds above the bottom molecule. They are supposed to be “parallel” to those above. On v1.99.0, the structure could not be further optimized.
