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Selecting constrains


#1

Greetings !

With my students we are emulating the propane conformation analysis, what is known topic in Organic Chemistry.

As we found, all given constraints in the list are active, therefore for each torsion angle one has to set up own constraint and delete the previous.

For smooth calculations we would welcome the possibility to create list of constraints and select(activate) some of them for calculations. This would enable us to prepare torsion angles constraints in advance and simply click on the constraint to activate it for the geometry optimization.

It would help at least if given constraints are editable.

Also, options save and load are not working… Would be good to have them working.

I think that the conformation analysis, as taught at Organic chemistry courses, is nice teaching example with Avogadro.


#2

As a student of associate professor Miroslav_Ilias I would like to support and also suggest some changes, it would be nice to add to the constraints section not only the option “Delete all” and “Delete Selected”, but also an editing tool, where we could change the value of one constraint when we want to work with the same indices.

As asssociate professor has mentioned, the calculations would be much smoother and faster by our work with torsion angles. The option, where we could select the constraints from the list and choose which of them would be “active” by calculations would be also very helpful.

I would like to appreciate the use of Avogadro by our molecular modelling course.


#3

Thanks for your question and suggestions. Certainly reworking the constraints are useful.

You can go into the properties (bonds, angles, torsions) and set particular values - here, I’ve clicked on a torsion (i.e., a particular row) and then clicked the value to edit it:

Which is to say that you can rotate one dihedral at a time to talk about conformer energies. Not sure if that completely solves your request, but it’s what I do when talking about conformational analysis.