Single point energy calculations

General Discussion
1

Hello. I have a question about single point energy calculations in Avogadro1.98.1. Are they possible? I’m teaching an online computational chemistry course and previously used Avogadro 1.2.0 to do this.

For example, I have the students build a simple molecule such as water. They then optimize the geometry using the MMFF94 force field. Next, I have them set one of the O-H bond lengths to 1.1 Å, and recalculate the energy at that geometry, set the bond to 1.2 Å, calculate the energy, etc. They then do the same thing, varying the H-O-H angle. This allows the students by hand to map out the potential energy and from that estimate the force constants used in the force field.

The process I just described was easy in Avogadro 1.2.0. I don’t see a way to do it in Avogadro2, but I admit that I have just started using it because some students are having difficulty installing Avogadro 1.2.0 on Windows 11, and am looking for a solution or work-around. The only single point energy calculation that I see uses the LJ potential model and no other force fields are able to be selected. From the Open Babel option, the geometry can be optimized with a specified force field, but I do not see a way to calculate the energy at some fixed geometry.

(We also use the auto-optimize feature in Avogadro 1.2.0 for things like this: Molecular Modeling Basics: The AutoOpt tool in Avogadro, so I really hoped that Avogadro 1.2.0 would not have installation problems this semester.)

Anyway, thanks in advance for any assistance.

2

Sorry, that’s on me - I thought I added that for 1.98.1 … I can add that for 1.99, which I hope to release later this month.

The new “Calculate” options represent a new framework for energies / geometry optimizations. In 1.98, you need Python and additional tools (e.g., beyond force fields) but I wasn’t able to get the Open Babel pieces integrated … and didn’t want to holdup the whole release.

3

Thanks for the information on single energy calculations.

Another difference between the versions that I noticed in energy calculations is that a ‘Messages’ window appears at the bottom of the screen in Avogadro 1.2.0 but not in Avogadro 1.98.1. This window is useful in providing the force field components of the energy (i.e., broken down in terms of the energy due bonds, angles, torsions, non-bonded interactions, etc.). This is great to be able to access when having students compare the results from one force field to another.

Is there somewhere in Avogadro2 that this information is easily accessible?

4

No, and that’s going to be somewhat hard to replicate outside of Open Babel. I can see the use for teaching, but not every program provides that. I’ll think if there’s a good way to bring that back.